Device, System, And Method For Depositing Processed Immiscible-Fluid-Discrete-Volumes

ABSTRACT

Various embodiments relate to systems and/or methods for sample preparation that can be used for biochemical and/or molecular biology procedures involving small volumes, for example, micro volumes or smaller. Methods and systems that can reduce sample size requirements and increase the number of samples on a substrate are provided. Samples can be applied to a plate or other appropriate substrate and can be used for, inter alia, sequencing reactions. In some embodiments, apparatuses, systems, and/or methods for charged analyte collection are provided. Charged analytes in a sample can be electrokinetically collected or extracted from a conduit through a hole formed in a sidewall of the conduit, by application of an electric field that causes the charged analytes to migrate in a direction that is transverse to the conduit.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims the benefit of earlier filed U.S.Provisional Patent Application No. 60/710,167, filed Aug. 22, 2005, U.S.Provisional Patent Application No. 60/731,133, filed Oct. 28, 2005, andU.S. Provisional Patent Application No. 60/818,197, filed Jun. 30, 2006,which are incorporated herein in their entireties by reference.

INTRODUCTION

The section headings used herein are solely for organization purposesand are not to be construed as limiting the subject matter described inany way.

Large scale sequencing projects can involve cloning DNA fragments inbacteria, picking and amplifying those fragments, and performingindividual sequencing reactions on each clone. Standard sequencingreactions can often be performed in 5 μl to 20 μl reaction volumes, eventhough only a small fraction of the sequencing product can be analyzed.Such cloning and sequencing protocols can be time consuming and can userelatively large sample and reagent volumes. The relatively largevolumes can be wasteful in terms of expensive consumable reagents, andinput sample quantity.

SUMMARY

Various embodiments of the present teachings relate to systems,apparatus, and/or methods for sample preparation that can be used forbiochemical or molecular biology procedures involving different volumes,for example, small volumes such as micro-liter sized volumes or smaller.

According to the present teachings, the system can comprise an apparatusfor generating discrete volumes of at least a first fluid in contactwith a second fluid, wherein the first and second fluids are immisciblewith each other, for example, discrete volumes of an aqueous liquid(herein “aqueous immiscible-fluid-discrete-volumes”), spaced-apart fromone another by a spacing fluid that is immiscible with theimmiscible-fluid-discrete-volumes. An immiscible-fluid-discrete-volumecan be a partitioned segment in which molecular biology procedures canbe performed. As used herein, an immiscible-fluid-discrete-volume can beone of many structures, three of which are: a fluid segment, a slug, andan emulsified droplet. In some embodiments,immiscible-fluid-discrete-conduits are formed and/or processed in aconduit.

This paragraph defines a conduit as it is used herein. A conduit can beany device in which an immiscible-fluid-discrete-volume can begenerated, conveyed, and/or flowed. For example, a conduit as definedherein can comprise any of a duct, a tube, a pipe, a channel, an opentop channel, a dosed channel, a capillary, a hole or another passagewayin a solid structure, or a combination of two or more of these, as longas the spaces defined by the respective solid structures are in fluidcommunication with one another. A conduit can comprise two or more tubesor other passageways connected together, or an entire system ofdifferent passageways connected together. An exemplary conduit cancomprise an immiscible-fluid-discrete-volume-forming tube, thermalspirals, valve passageways, a processing conduit, junctions, and thelike components all connected together to form one or more fluidcommunications therethrough, which system is also referred to herein asa main processing conduit. Examples of solid structures with holes orpassageways therein that can function as conduits are manifolds,T-junctions, Y-junctions, rotary valves, and other valves. Thus, whenconnected to conduits, such structures can be considered part of aconduit as defined herein.

This paragraph defines a fluid segment, as it is used herein. A fluidsegment is a discrete volume that has significant contact with one ormore conduit wall(s), such that a cross-sectional area of the fluidsegment is the same size and shape as the cross-sectional area of theconduit it contacts. At least a portion of a fluid segment fully fillsthe cross-sectional area of the conduit, such that the immiscible fluidadjacent it in the conduit can not flow past the fluid segment. Theentire longitudinal length of the fluid segment may not contact theconduit walls.

This paragraph defines a slug as used herein. A slug is a discretevolume that has at least a portion of which has approximately the samecross-sectional shape as the conduit in which it exists, but a smallersize. The smaller size is due to the insignificant contact, if any, ofthe slug with the conduit wall(s). A slug can have a cross-sectionaldimension between approximately 0.5 and approximately 1.0 times themaximum dimension of a cross sectional area of the conduit. If theconduit has a circular cross section, the cross-sectional area of a slugcan be concentric with the conduit's cross-sectional area, but it doesnot have to be, such as, for example, when the conduit is horizontaland, due to different specific gravities, one fluid rises toward the topof the cross-sectional area of the conduit under the influence ofgravity. A slug can be free of contact with the conduit walls. When notmoving relative to the conduit, a slug can have “feet” that appear asnibs or bumps along an otherwise smoothly appearing round surface. It istheorized that the feet at the bottom of the slug may have contact withthe conduit wall. In contrast to a fluid segment, the contact a slug canhave with the conduit wall(s) still permits the immiscible fluidadjacent it in the conduit to flow past the slug.

The “slugs” formed by the teachings herein, separated by spacing fluid,can merge together to form larger slugs of liquid, if contactedtogether. The ability of the slugs, for example, aqueous slugs,described and taught herein, to merge together with each other,facilitates the downstream addition of aqueous reagents to the slugs.

This paragraph defines an emulsified droplet, as used herein. Anemulsified droplet is a discrete volume that has no contact with thewalls of the conduit. The size of an emulsified droplet is notnecessarily constrained by the conduit, and examples of emulsifieddroplets described in the prior art range in size from about 1femtoliter to about 1 nanoliter. The shape of an emulsified droplet isnot constrained by the conduit, and due to the difference in surfaceenergies between it and the continuous phase liquid in which it isdispersed, it is generally spherical. It can have a maximum dimensionthat is not equal to, nor approximately equal to, but much less than themaximum dimension of the cross-sectional area of the conduit, forexample, 20%, 10%, 5% or less. As described in the prior art, emulsifieddroplets typically range in volume from about 1 femtoliter to about 1nanoliter. An emulsified droplet will not merge upon contact withanother emulsified droplet to form a single, larger discrete volume,without external control. Put another way, an emulsified droplet is astable discontinuous phase in a continuous phase.

A conduit can contain more than one emulsified droplet, but not morethan one slug or fluid segment, at any cross-sectional location. Thus, afirst emulsified droplet may not necessarily impede the movement of asecond emulsified droplet past it, where as a fluid segment and a slugnecessarily do not permit the passage of another fluid segment or slugpast them, respectively. If two fluid segments are separated by a fluidwith which the first and second of the two fluids is each immiscible,then the immiscible fluid also forms a discrete volume. It is likelythat it has significant contact with the conduit walls and thus isanother fluid segment.

Whether two immiscible fluids, when present in a conduit, form fluidsegments of the first and second of the two immiscible fluids, slugs ofthe first immiscible fluid, or emulsified droplets of the firstimmiscible fluid depends on at least the method of introduction of eachfluid into the conduit, the relative surface energies of the firstimmiscible fluid, the second immiscible fluid, and the conduit material,and the contact angle each forms with the other two materials,respectively, and the volume of the first immiscible fluid. Thus, it isrecognized that these definitions are merely reference points on acontinuum, the continuum of the shape and size of discrete volumes of afirst immiscible fluid in a conduit, and discrete volumes will existthat, when described, fall between these definitions.

The molecular biology procedures can, for example, utilize proteins ornucleic acids. Procedures with nucleic acids can comprise, for example,a PCR amplification and/or nucleic acid analysis of an amplificationproduct. The PCR amplification and/or nucleic acid analysis of anamplification product can comprise an integrated DNA amplification/DNAsequencing method.

Using the apparatus, methods, and/or systems provided in thisapplication, a polymerase chain reaction (PCR) amplification of singleDNA molecules can be performed, for example, to obtain amplicons. Theamplified DNA or amplicons can then be used in a sequencing reaction andthen be sequenced in small volumes. Other manipulations of nucleic acidsor proteins can also be accomplished, for example, DNA hybridizationreactions or antibody-antigen binding assays.

The apparatus, system and/or methods described herein can also be usedin conjunction with U.S. Provisional Patent Application No. 60/710,167entitled “Sample Preparation for Sequencing” to Lee et al., filed Aug.22, 2005 (Attorney Docket No. 5841P), U.S. Provisional PatentApplication No. 60/731,133 entitled “Method and System for Spot Loadinga Sample” to Schroeder et al., filed Oct. 28, 2005 (Attorney Docket No.5010-288), and systems described in U.S. Provisional Patent ApplicationNo. 60/818,197 filed Jun. 30, 2006, each of which are incorporatedherein in their entireties by reference.

An exemplary type of sample preparation can be used for genotyping,gene-expression, methylation analysis, and/or directed medicalsequencing (VariantSEQr™, for example) that requires multiple liquids tobe brought together in an aqueous discrete volume. For example, in agene-expression application, each aqueous discrete volume can containindividual primer sets. The sample to be analyzed, for example,complementary DNA (cDNA), can be added to each aqueous discrete volume.In the VariantSEQr™ application, for example, an aqueous discrete volumecan comprise a primer set and genomic DNA can be added to that discretevolume According to various embodiments, a system and method areprovided that are able to process discrete volumes with unique content.According to various embodiments of the present teachings, spitting,dropping, or other techniques to discharge immiscible-liquid, discretevolumes can be used. According to various embodiments, animmiscible-liquid, discrete volume of at least an aqueous sample fluidcan be discharged from a tube.

According to various embodiments, a system is provided comprising: atleast one conduit; a substrate separate from and spaced from the atleast one conduit, the substrate comprising an electrically conductivesurface; and an apparatus for moving in a predetermined pattern relativeto one another, the substrate and the at least one conduit.

According to various embodiments, a system is provided comprising: anaqueous sample injection unit in fluid communication with at least oneconduit comprising a maximum inner cross-sectional dimension; a spacingfluid injection unit in fluid communication with the at least oneconduit, the aqueous sample injection unit and the spacing fluidinjection unit comprising separate units each in fluid communicationwith the at least one conduit; a control unit adapted to flow an aqueoussample and a spacing fluid from the aqueous sample injection unit andthe spacing fluid injection unit, respectively, and adapted to injectvolumes of aqueous sample and spacing fluid that respectively form slugsin the at least one conduit wherein each slug has an outer dimensionthat is equal to the maximum inner cross-sectional dimension of the atleast one conduit; an electrically conductive substrate; and a capillaryelectrophoretic sequencer adapted to inject a sample component when asample component is disposed on the electrically conductive surface.

According to various embodiments, a method is provided comprising:forming a plurality of aqueous sample slugs spaced apart from oneanother by slugs of spacing fluid in a conduit, at least one of theaqueous sample slugs comprising at least one target analyte; anddispensing the aqueous sample slugs one-at-a-time from the conduit ontoa substrate to form a pattern of spaced apart aqueous samples on thesubstrate, the substrate comprising an electrically conductive surface.

According to various embodiments, a method is provided comprising:forming in a conduit a plurality of aqueous sample slugs, at least oneof the aqueous sample slugs comprising at least one target analytecomprising at least one respective linkage group; and dispensing theaqueous sample slugs one-at-a-time from the conduit onto a substrate toform a pattern of aqueous samples on the substrate, the substratecomprising an electrically conductive surface adapted to bind the atleast one respective linkage group to form an attached analyte.

According to various embodiments, a method is provided comprising:amplifying DNA in a plurality of aqueous sample slugs in a conduit toform amplicons, each aqueous slug separated from an adjacent aqueousslug by at least one oil slug; moving or rastering the conduitcomprising the amplicons over a substrate and depositing the ampliconsfrom the conduit onto the substrate, the substrate comprising anelectrically conductive surface; attaching the amplicons to theelectrically conductive surface; contacting the substrate with asequencing reaction mixture to form at least one dye-labeled spot;positioning a capillary of a capillary electrophoretic analyzer over theat least one dye-labeled spot; electrically contacting the dye-labeledspot with the capillary; and injecting one or more components from thedye-labeled spot into the capillary.

According to various embodiments, a method is provided comprising:dispensing DNA into a plurality of aqueous sample slugs in a conduit,each aqueous slug separated from an adjacent aqueous slug by at leastone non-aqueous slug; moving or rastering the conduit comprising the DNAover a substrate and depositing the DNA from the conduit onto thesubstrate, the substrate comprising an electrically conductive surface;attaching the DNA to the electrically conductive surface; contacting theelectrically conductive surface with a reaction mixture; positioning acapillary tube over the attached DNA; electrically contacting the DNAwith the capillary tube; and injecting the DNA into the capillary tube.

According to various embodiments, the present teachings provide a systemcomprising at least one transport conduit, the at least one transportconduit comprising at least one sidewall. In some embodiments, thesystem can comprise a through hole formed through the at least onesidewall. In some embodiments, the system can comprise a charged analytecollection chamber in fluid communication with the through hole. In someembodiments, the system can comprise a positive electrode. In someembodiments, the system can comprise negative electrode. In someembodiments, the system can comprise a power source, wherein thepositive electrode, the negative electrode, and the power source areconnected together and configured to form an electric field extendingfrom the transport conduit, through the through hole, and to the chargedanalyte collection chamber, and of sufficient strength to cause acharged analyte in the transport conduit to electrokinetically migratethrough the through hole toward the charged analyte collection chamber.

According to various embodiments, the present teachings provide a methodcomprising moving a sample comprising a charged analyte through atransport conduit and into alignment with a portion of the transportconduit comprising a through hole formed in a sidewall thereof. In someembodiments, the method can comprise generating an electric field thatextends through the through hole. In some embodiments, the method cancomprise electrokinetically migrating the charged analyte from thetransport conduit and through the through hole.

According to various embodiments, the present teachings provide a systemcomprising an immersion plate, and a layer of a first fluid retained bythe immersion plate. In some embodiments, the system can comprise aconduit comprising a tip and an interior, the interior comprising aplurality of immiscible-fluid-discrete-volumes of a second fluid, spacedapart by a spacing fluid that is immiscible with each of theimmiscible-fluid-discrete-volumes, disposed in the interior, wherein thetip is positioned such that when the immiscible-fluid-discrete-volumesexit the tip, the immiscible-fluid-discrete-volumes contact the firstfluid retained by the immersion plate, and the second fluid has adifferent density than the first fluid.

According to various embodiments, the present teachings provide a methodcomprising discharging immiscible-fluid-discrete-volumes from inside aconduit having a discharge tip, through the discharge tip, and into afirst fluid retained by an immersion plate, wherein the first fluid isimmiscible with the immiscible-fluid-discrete-volumes and the density ofthe first fluid is different than the densities of each of theimmiscible-fluid-discrete-volumes.

According to various embodiments, the present teachings provide a systemcomprising a dispensing conduit comprising a discharge tip. In someembodiments, the system can comprise a set ofimmiscible-fluid-discrete-volumes spaced-apart from one another by aspacing fluid that is immiscible with theimmiscible-fluid-discrete-volumes, disposed in the conduit. In someembodiments, the system can comprise a negative pressure source disposedadjacent the discharge tip.

According to various embodiments, the present teachings provide a methodof dispensing immiscible-fluid-discrete-volumes, comprising providing adispensing conduit comprising a dispensing tip, and a set ofimmiscible-fluid-discrete-volumes spaced-apart from one another by aspacing fluid that is immiscible with theimmiscible-fluid-discrete-volumes. In some embodiments, the method cancomprise providing a waste removal conduit adjacent the dispensing tip.In some embodiments, the method can comprise applying a vacuum to thewaste removal conduit. In some embodiments, the method can comprisedetecting a first immiscible-fluid-discrete-volume, that contains ananalyte of interest, from the set of immiscible-fluid-discrete-volumes.In some embodiments, the method can comprise removing the vacuum. Insome embodiments, the method can comprise dispensing the firstimmiscible-fluid-discrete-volume.

According to various embodiments, the present teachings provide a systemcomprising a conduit comprising a tip. In some embodiments, the systemcan comprise a plurality of immiscible-fluid-discrete-volumes disposedin the conduit and spaced apart from one another by a spacing fluid thatis immiscible with each of the plurality ofimmiscible-fluid-discrete-volumes. In some embodiments, the system cancomprise a capillary electrophoresis capillary, positioned adjacent tothe tip of the conduit, the capillary electrophoresis capillary havingan injection tip, wherein the capillary electrophoresis capillary andthe conduit are axially aligned with one another.

According to various embodiments, the present teachings provide a methodcomprising discharging immiscible-fluid-discrete-volumes from a tip of aconduit directly into a capillary electrophoresis capillary, the conduitcomprising a plurality of immiscible-fluid-discrete volumes spaced apartfrom one another by a spacing fluid that is immiscible with each of theimmiscible-fluid-discrete-volumes.

According to various embodiments, the present teachings provide a methodcomprising discharging immiscible-fluid-discrete-volumes from conduitand into an injector of a capillary electrophoresis apparatus, whereinat an interface between the conduit and the injector one or morecomponents in the immiscible-fluid-discrete-volumes is concentrated bydielectrophoresis before entering the injector.

The molecular biology procedures that can be performed on the variousdiscrete volumes described herein, prior to out-processing as describedherein, can, for example, utilize proteins or nucleic acids. Procedureswith nucleic acids can comprise, for example, a PCR amplification and/ornucleic acid analysis of an amplification product. The PCR amplificationand/or nucleic acid analysis of an amplification product can comprise anintegrated DNA amplification/DNA sequencing method.

Using the apparatus, methods, and/or systems provided in thisapplication, a polymerase chain reaction (PCR) amplification of singleDNA molecules can be performed, for example, to obtain amplicons. Theamplified DNA or amplicons can then be used in a sequencing reaction andthen be sequenced in small volumes. Other manipulations of nucleic acidsor proteins can also be accomplished, for example, DNA hybridizationreactions or antibody-antigen binding assays.

The apparatus, system and/or methods described herein can also be usedin conjunction with U.S. Provisional Patent Application No. 60/710,167entitled “Sample Preparation for Sequencing” to Lee et al., filed Aug.22, 2005 (Attorney Docket No. 5841P), U.S. Provisional PatentApplication No. 60/731,133 entitled “Method and System for Spot Loadinga Sample” to Schroeder et al., filed Oct. 28, 2005 (Attorney Docket No.5010-288), and systems described in U.S. Provisional Patent ApplicationNo. 60/818,197 filed Jun. 30, 2006, which are incorporated herein intheir entireties by reference.

An exemplary type of sample preparation can be used for genotyping,gene-expression, methylation analysis, and/or directed medicalsequencing (VariantSEQr™, for example) that requires multiple liquids tobe brought together in an aqueous discrete volume. For example, in agene-expression application, each aqueous discrete volume can containindividual primer sets. The sample to be analyzed, for example,complementary DNA (cDNA), can be added to each aqueous discrete volume.In the VariantSEQr™ application, for example, an aqueous discrete volumecan comprise a primer set and genomic DNA can be added to that discretevolume.

In some embodiments, a first conduit can have an inner diameter, and theinner diameter can be from about 10 microns to about 2000 microns. Asecond conduit can have an inner diameter, and the inner diameter can befrom about 20 microns to about 5000 microns, and can be large enough toaccommodate the outer periphery of the first conduit.

Various embodiments of the present teachings relate to an apparatus,system, or method for sample preparation and/or sample deposition. Thesample preparation can be used for biochemical or molecular biologyprocedures involving small volumes, for example, microliter-sizedvolumes or smaller. The system can comprise an apparatus comprising atleast two coaxially arranged tubes in fluid communication with pump(s)for providing immiscible-fluid-discrete-volumes of a first liquidseparated by a second fluid, for example,immiscible-fluid-discrete-volumes of water or an aqueous-based liquid,separated by oil. The immiscible-fluid-discrete-volumes can form smallpartitioned segments to be used in molecular biology procedures. Themolecular biology procedures can comprise, for example, a PCRamplification and/or nucleic acid analysis of the amplification product.The PCR amplification and/or nucleic acid analysis of the amplificationproduct can comprise an integrated DNA amplification/DNA sequencingmethod.

Using the apparatus, methods, and/or systems provided in thisapplication processes can be performed on theimmiscible-fluid-discrete-volumes. These downstream processes caninclude, for example, electrophoretic separation, fluorescent detection,and the like. Other manipulations of nucleic acids or proteins can alsobe accomplished, for example, DNA hybridization reactions orantibody-antigen binding assays.

An apparatus is provided that can be used for different types of samplepreparation and sample processing. For example, the apparatus can beused 1) to prepare spaced-apart aqueousimmiscible-fluid-discrete-volumes separated by an immiscible spacingfluid, for example, oil, for carrying out reactions in microliter-sizedor smaller volumes, 2) for manipulating samples of interest inimmiscible-fluid-discrete-volumes and then depositing them into samplewells, or 3) for rinsing a conduit tip between depositing a first volumeand depositing a second volume, to avoid contamination of the secondvolume with the first volume.

According to various embodiments, flow rates for preparing aqueousimmiscible-fluid-discrete-volumes can comprise rates of from about 1picoliter/sec. to about 200 microliters/sec., and can be selected basedon the inner diameter of the conduits through which the liquids are tobe pumped. Tubing that can be used with this flow rate can comprise aninner diameter of from about 250 microns to about 1000 microns. In otherembodiments, the inner diameter of the inner tube can be from about 10microns to about 2000 microns, while the inner diameter of the outertube can be from about 20 microns to about 5000 microns, for example,from about 35 microns to about 500 microns. Other diameters, however,can be used based on the characteristics of theimmiscible-fluid-discrete-volume formation or rinsing system desired. Insome embodiments, a tube having a 10 micron inner diameter is used witha flow rate of from about 8 to about 10 picoliters/second. In someembodiments, a tube having a 5000 micron inner diameter is used with aflow rate of from about 25 to about 200 microliters/second. In someembodiments, a tube having a 500 micron inner diameter is used with aflow rate of from about 0.25 to about 2.0 microliters/second.

In other embodiments, for example, when an apparatus of the presentteachings is used in a triage function for rinsing the tip of, forexample, the inner tube of an apparatus, the flow rate can comprise arate from about 0.1 microliter/sec. to about 1.0 microliter/sec.

According to various embodiments, a method is provided that uses anapparatus comprising coaxially arranged tubes. The method comprisescontacting an aqueous sample liquid with a non-aqueous spacing fluidthat is immiscible with the aqueous sample to form a plurality ofisolated portions of the aqueous sample in a capillary channel separatedfrom one another by the non-aqueous spacing fluid. The aqueous sampleliquid can comprise a plurality of target nucleic acid sequences,wherein at least one of the isolated portions comprises at least onetarget nucleic acid sequence. In some embodiments, at least 50% of theplurality of the isolated portions in the inner conduit can eachcomprise a single target nucleic acid sequence. In various otherembodiments, less than about 50% of the plurality of isolated portionsin the capillary channel can each comprise a single target nucleic acidsequence. In other embodiments, at least 1% or more, 5% or more, 10% ormore, or 20% or more can have a single target nucleic acid sequence, forexample, upon formation of the isolated portions.

According to various embodiments, each of the plurality of isolatedimmiscible-fluid-discrete-volumes in the inner conduit can comprise oneor more respective oligonucleotide primers. Oligonucleotide primers canbe chosen as determined by one of skill in the art to accomplish thedesired objective, for example, universal primers can be used.

In some embodiments, out-putting immiscible-fluid-discrete-volumes thathave been subjected to upstream processing, can be integrated with thesystem. Such upstream processing can include amplifying the at least onetarget nucleic acid sequence in the first isolated portion in thecapillary channel to form an amplicon, and thereafter subjecting theamplicon to a nucleic acid sequencing reaction. For such purposes, andin some embodiments, the isolated portions orimmiscible-fluid-discrete-volumes can comprise reaction components, forexample, oligonucleotide primers. Various embodiments of processing caninclude universal PCR that can comprise up-front multiplexed PCRfollowed by decoding, for example, see WO 2004/051218 to Andersen etal., U.S. Pat. No. 6,605,451 to Marmaro et al., U.S. patent applicationSer. No. 11/090,830 to Andersen et al., and U.S. patent application Ser.No. 11/090,468 to Lao et al., all of which are incorporated herein intheir entireties by reference. Details of real time PCR can be found inHiguchi et al., U.S. Pat. No. 6,814,934 B1, which is incorporated hereinby reference in its entirety.

According to various embodiments, once the steps of a desired protocol,for example, a PCR, PCR clean-up, and sequencing reaction protocol, havebeen completed, a sample can be removed or injected from a processingconduit, for example, using an electrical field applied across a channeland extending into a charged analyte collection chamber or compartment,or by using another electrokinetic sample movement technique. Thecollected or extracted charged analytes removed from the sample can thenbe used for DNA sequencing or other procedures. The DNA sequencing canuse capillary electrophoresis instruments, for example, a commerciallyavailable AB 3730×1 DNA Analyzer (Applera Corporation, Foster City,Calif.), that can process samples in 96- or 384-well plate formats. Invarious embodiments, the sample can be removed, injected, or recoveredfrom the processing conduit into one or more wells of a microtiterplate, for example, through a pathway that comprises a loading channelor tube.

Further devices, systems, and methods that can be used with or otherwiseimplement the present teachings include those described, for example, inU.S. patent application Ser. No. ______, filed Aug. 22, 2006, entitled“Apparatus, System, and Method Using Immiscible-Fluid-Discrete-Volumes,”to Lee et al. (attorney docket number 5010-362), in U.S. patentapplication Ser. No. ______, filed Aug. 22, 2006, entitled “Device andMethod for Making Discrete Volumes of a First Fluid in Contact with aSecond Fluid Which are Immiscible with Each Other” to Cox et al.(attorney docket number 5010-363), and in U.S. patent application Ser.No. ______, filed Aug. 22, 2006, entitled “Apparatus and Method of Micofluidic Control of Discrete Volumes of a First Fluid in Contact With aSecond Fluid, Wherein the First and Second Fluids are Immiscible,” toCox et al, (attorney docket number 6406 US), which are hereinincorporated in their entireties by reference.

DRAWINGS

The skilled artisan will understand that the drawings described below,are for illustration purposes only. The drawings are not intended tolimit the scope of the present teachings in any way. In the drawings:

FIGS. 1A and 1B are the left-side and right-side, respectively, of aschematic diagram depicting a system according to various embodiments ofthe present teachings and configured to generateimmiscible-fluid-discrete-volumes of a first fluid spaced apart from oneanother by a spacing fluid, to process theimmiscible-fluid-discrete-volumes, and to output theimmiscible-fluid-discrete-volumes;

FIG. 1C is a simplified block diagram of a system configured to includeembodiments described herein and to process the generatedimmiscible-fluid-discrete-volumes and to output theimmiscible-fluid-discrete-volume;

FIG. 2 is a cross-sectional side view of animmiscible-fluid-discrete-volume collection system comprising animmersion plate, according to various embodiments;

FIG. 3 is an enlarged cross-sectional side view of section A taken fromFIG. 2;

FIG. 4A illustrates a cross-sectional view of the inner tube positionedwith its end surface beyond the end surface of the outer tube and ablock that forms part of the tip rinsing apparatus, according to variousembodiments;

FIG. 4B illustrates a cross-sectional view of the inner tube positionedwith respect to the outer tube such that the end surface of the innertube is flush with the end surface of the outer tube, whereby the blockcan be used to rinse the conduit tip after a sample deposition step;

FIG. 5A illustrates a cross-sectional view of removal of waste material,according to various embodiments;

FIG. 5B illustrates a cross-sectional view of using the apparatus todeposit a sample in a sample well, according to various embodiments;

FIG. 6 illustrates a cross-sectional view of a system incorporating anapparatus of FIGS. 4A and 4B to depositimmiscible-fluid-discrete-volumes for downstream sample processing asdesired, according to various embodiments;

FIG. 7 is a cross-sectional side view of a system comprising thedischarge tip of an immiscible-fluid-discrete-volume-containing conduitaxially aligned with and adjacent the injection tip of an injector of acapillary electrophoresis capillary, according to various embodiments;

FIG. 8A is a cross-sectional side view of a system comprising thedischarge tip of an immiscible-fluid-discrete-volume-containing conduitand three different injection tips of three respective capillaryelectrophoresis capillaries; according to various embodiments;

FIG. 8B is an enlarged cross-sectional axial view of an injector of acapillary electrophoresis capillary useful with the systems shown inFIGS. 7 and 8A, according to various embodiments;

FIG. 9 is a cross-sectional side view of a system comprising thedischarge tip of an immiscible-fluid-discrete-volume-containing conduitaxially aligned with and adjacent a dielectrophoresis device andarranged for processing of a discrete volume with the dielectrophoresisdevice, according to various embodiments;

FIGS. 10A, 10B, and 10C are cross-sectional side views of varioussystems each comprising the discharge tip of animmiscible-fluid-discrete-volume-containing conduit axially aligned withand adjacent a dielectrophoresis device and arranged for processing of adiscrete volume with the dielectrophoresis device, according to variousembodiments;

FIG. 11 is a perspective view of a system for applying samples in araster pattern to an electrically conductive substrate;

FIG. 12 is a perspective view of a system comprising an electricallyconductive surface receiving samples that have been amplified by PCRreaction.

FIG. 13 is a perspective view of a system comprising a substrate havinga zig-zag channel for receiving samples.

FIG. 14 illustrates a simplified protocol for sequencing products beingapplied to an electrically conductive surface and then beingelectroinjected into capillaries.

FIG. 15 illustrates a method of DNA analysis with subsequent depositiononto a substrate in preparation for injection and further analysis;

FIG. 16 provides an enlargement of part of FIG. 15 showing samplemigration, for example, electrokinetically injected sample, moving intocapillary tubes.

FIG. 17 illustrates injection of sample portions into capillaryelectrophoresis channels;

FIG. 18 illustrates a perspective view of a system for moving discretevolumes of fluid along electro-wetting pathways to an intake locationadjacent a tip of a fluid processing conduit, such as an injector of acapillary electrophoretic injector;

FIG. 19 illustrates electrokinetic sample collection from a slug in achannel wherein an opening in a tubular wall can allow electricalcurrent to pass through a slug, causing negatively charged molecules tomigrate toward a positively charged electrode, and positively chargedmolecules to migrate toward a negatively charged electrode;

FIG. 20 illustrates a multiplexing scheme for electrokinetic samplecollection from slugs in a channel;

FIG. 21 illustrates electrokinetic sample collection from slugs in onechannel into another channel;

FIG. 22A illustrates a system for electrokinetic sample collectionaccording to various embodiments, in which DNA or other analytes aredriven into collection tubes by an electric field applied across atransport channel;

FIG. 22B illustrates an enlarged view of section 22B shown in FIG. 22A.

FIGS. 23-28 are top views of various stator and rotor valve systemsaccording to various embodiments;

FIG. 29 is a top view of a slider-in-housing valve that can form orinterrupt a three-way fluid communication, according to variousembodiments; and

FIGS. 30 and 31 are perspective views of a system for depositing aqueousdiscrete volumes in a sample tray and removing waste.

DESCRIPTION OF VARIOUS EMBODIMENTS

It is to be understood that the following descriptions are exemplary andexplanatory only. The accompanying drawings are incorporated in andconstitute a part of this application and illustrate several exemplaryembodiments with the description. Reference will now be made to variousembodiments, examples of which are illustrated in the accompanyingdrawings. Wherever possible, the same reference numbers are used in thedrawings and the description to refer to the same or like parts.

Throughout the application, descriptions of various embodiments use“comprising” language, however, it will be understood by one of skill inthe art, that in some specific instances, an embodiment canalternatively be described using the language “consisting essentiallyof” or “consisting of.”

For purposes of better understanding the present teachings and in no waylimiting the scope of the teachings, it will be clear to one of skill inthe art that the use of the singular includes the plural unlessspecifically stated otherwise. Therefore, the terms “a,” “an” and “atleast one” are used interchangeably in this application.

Unless otherwise indicated, all numbers expressing quantities,percentages or proportions, and other numerical values used in thespecification and claims, are to be understood as being modified in allinstances by the term “about.” Accordingly, unless indicated to thecontrary, the numerical parameters set forth in the followingspecification and attached claims are approximations that can varydepending upon the desired properties sought to be obtained. In someinstances, “about” can be understood to mean a given value±5%.Therefore, for example, about 100 nl, could mean 95-105 nl. At the veryleast, each numerical parameter should at least be construed in light ofthe number of reported significant digits and by applying ordinaryrounding techniques.

The term “coaxially arranged” should be understood to mean at least twoconduits are arranged one inside the other, for example, such that theyhave a common axis. An example of a coaxial arrangement can comprise asmaller diameter tube within a larger diameter tube.

Reference to “nucleotide” should be understood to mean a phosphate esterof a nucleotide, as a monomer unit or within a nucleic acid. Nucleotidesare sometimes denoted as “NTP”, or “dNTP” and “ddNTP” to particularlypoint out the structural features of the ribose sugar. “Nucleotide5′-triphosphate” can refer to a nucleotide with a triphosphate estergroup at the 5′ position. The triphosphate ester group can includesulfur substitutions for the various oxygens, for example,α-thio-nucleotide 5′-triphosphates. Nucleotides can comprise a moiety ofsubstitutes, for example, see, U.S. Pat. No. 6,525,183 B2 to Vinayak etal., incorporated herein by reference in its entirety.

The terms “polynucleotide” or “oligonucleotide” or “nucleic acid” can beused interchangeably and includes single-stranded or double-strandedpolymers of nucleotide monomers, including 2′-deoxyribonucleotides (DNA)and ribonucleotides (RNA) linked by internucleotide phosphodiester bondlinkages, or internucleotide analogs, and associated counter ions, forexample, H⁺, NH₄ ⁺, trialkylammonium, Mg²⁺, Na⁺ and the like. Apolynucleotide can be composed entirely of deoxyribonucleotides,entirely of ribonucleotides, chimeric mixtures thereof. Polynucleotidescan be comprised of nucleobase and sugar analogs. Polynucleotidestypically range in size from a few monomeric units, for example, 5-40when they are frequently referred to in the art as oligonucleotides, toseveral thousands of monomeric nucleotide units. Unless denotedotherwise, whenever a polynucleotide sequence is represented, it will beunderstood that the nucleotides are in 5′ to 3′ order from left to rightand that “A” denotes deoxyadenosine, “C” denotes deoxycytidine, “G”denotes deoxyguanosine, and “T” denotes thymidine, unless otherwisenoted. A labeled polynucleotide can comprise modification at the5′terminus, 3′terminus, a nucleobase, an internucleotide linkage, asugar, amino, sulfide, hydroxyl, or carboxyl. See, for example, U.S.Pat. No. 6,316,610 B2 to Lee et al. which is incorporated herein byreference. Similarly, other modifications can be made at the indicatedsites as deemed appropriate.

The term “reagent,” should be understood to mean any reaction componentthat in any way affects how a desired reaction can proceed or beanalyzed. The reagent can comprise a reactive or non-reactive component.It is not necessary for the reagent to participate in the reaction. Thereagent can be a recoverable component comprising for example, a solventand/or a catalyst. The reagent can comprise a promoter, accelerant, orretardant that is not necessary for a reaction but affects the reaction,for example, affects the rate of the reaction. A reagent can comprise,for example, one member of a binding pair, a buffer, or a DNA thathybridizes to another DNA. The term “reagent” is used synonymous withthe term “reaction component.”

According to various embodiments, two immiscible fluids can form smallvolume slugs of one of the fluids in which biochemical reactions and/oranalyses can occur. As opposed to reactions in slugs, reactions inpartitioned sections have been discussed in U.S. Patent Publication2004/0180346 to Anderson et which is incorporated herein by reference inits entirety. Often, the partitioned sections can be found asmicrodroplets or globules or spheres in a non-constrained volume. Suchpartitioned sections have been used in various biochemical and molecularbiology procedures. Ghadessy et al., Nature Biotech. 22: 755-759 (2004),Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003), andUtada et al., Science 308:537-541 (2005), all of which are incorporatedherein by reference in their entireties.

Methods, apparatuses and systems described herein can use fluidsimmiscible in each other. Fluids can be said to be immiscible in eachother when they can be maintained as separate fluid phases underconditions being used. Immiscible fluids can also be said to beincapable of mixing with each other or attaining a solution with eachother. An aqueous liquid and a non-aqueous liquid such as oil can besaid to be immiscible with each other. Throughout the specification,reference is made to aqueous slugs. This is merely exemplary and doesnot necessarily preclude the use or manufacture of non-aqueous liquidslugs in combination with an immiscible liquid.

While oil and aqueous liquids are immiscible in each other, such acombination does not necessarily form aqueousimmiscible-fluid-discrete-volumes in the oil when the two liquids aremixed or placed together. For example, oil can form the disperse phasein a continuous aqueous liquid in a larger volume, as it does in certainsalad dressings. For another example, oil and aqueous liquids can merelyform aqueous droplets or microdroplets in a larger volume of oil, butnot necessarily aqueous immiscible-fluid-discrete-volumes. Aqueousimmiscible-fluid-discrete-volumes can form, however, using an apparatussuch as, for example, apparatus 100 as shown in FIGS. 2A, 2B, and 3.

Aqueous solutions and oil from separate sources can be combined to forma continuous flowing liquid stream comprising aqueousimmiscible-fluid-discrete-volumes separated from one another by the oil.Because the aqueous immiscible-fluid-discrete-volumes entirely or almostentirely fill the cross-sectional area of the conduit or tube in whichthey are formed, the resulting stream of aqueousimmiscible-fluid-discrete-volumes in oil can exhibit a bandedappearance. According to various embodiments, such a pattern can beexhibited by combining any two immiscible fluids with one another. Thepattern can be formed throughout the length of the conduit. In variousembodiments, a first aqueous immiscible-fluid-discrete-volume cancontain different reagents than a second aqueousimmiscible-fluid-discrete-volume. In other words, not all aqueousimmiscible-fluid-discrete-volumes throughout the conduit need to containthe same reagents.

An aqueous immiscible-fluid-discrete-volume can forcer a distinctsegment bounded by oil and the oil can space the contents of the aqueousinimiscible-fluid-discrete-volume from an adjacent aqueousimmiscible-fluid-discrete-volume. In various embodiments, liquids otherthan oil can act as a spacing fluid, provided that the spacing fluid andaqueous fluid are immiscible with respect to each other and providedthat they can form individual aqueous immiscible-fluid-discrete-volumesspaced apart from one another by the spacing fluid. In variousembodiments, gas can be used as a spacing fluid.

According to various embodiments, methods are provided that refer toprocesses or actions involved in sample preparation and analysis. Itwill be understood that in various embodiments a method can be performedin the order of processes as presented, however, in related embodiments,the order can be altered as deemed appropriate by one of skill in theart in order to accomplish a desired objective.

According to various embodiments, a system is provided that can be usedas a front-end sample preparation device for high-throughput sequencing,or other applications requiring preparation and/or processing of aplurality of small samples. The samples can comprise, for example,nucleic acids or proteins. The system can be integrated and/or adaptedto function with other pieces of equipment adapted for furtherprocessing of samples, for example, an ABI 310, ABI 3130, ABI 3130xl,ABI 3700, ABI 3730, or ABI 3730xl capillary electrophoretic analyzer(available from Applied Biosystems, Foster City, Calif.) that can beused for sequencing

According to various embodiments, a system is provided that can compriseat least one capillary channel, a substrate separate from and spacedapart from the at least one capillary channel, and an apparatus formoving in a predetermined pattern, relative to one another, thesubstrate and/or the at least one capillary channel. In variousembodiments, the capillary channel can comprise a capillary tube. Thesubstrate can comprise an electrically-conductive surface. In variousembodiments, the substrate can comprise linker moieties adapted to bindto a nucleic acid. In other embodiments, the substrate does notnecessarily comprise linker moieties.

According to various embodiments, a sample to be deposited on thesubstrate can comprise the linker moieties, while in other embodiments,the sample can comprise a binding partner for the linker moiety that isalready attached to the substrate. Examples of linker moieties and theirbinding partners can comprise, for example, biotin/streptavidin orstreptavidin/biotin combinations.

According to various embodiments, the system can comprise an apparatusfor detecting a sample bound to the substrate. The sample can be boundto the substrate through at least one of the linker moieties. A linkermoiety can comprise, for example, a thiol group. The at least one linkermoiety can comprise a plurality of the same linker moieties or aplurality of different linker moieties, that can comprise, for example,steptavidin moieties or biotin moieties. The electrically-conductivesurface can comprise, for example, a gold surface or a gold coating on abase structure. The predetermined pattern for moving an apparatus canbe, for example, a raster pattern. In various embodiments, otherelectrically conductive substrates or coatings on a base structure canbe used, for example, platinum substrates or coatings, palladiumsubstrates or coatings, alloy substrates or coatings, and the like. Thecoating can be segmented into several different sections, as might bedesirable when interfacing to a system with a smaller number ofcapillaries than the number of samples spotted, as when interfacing afour channel capillary system to a 384 position surface. These sectionscan correspond to the areas useful for performing a single injectionwith a desired instrument. In some embodiments, the entire coating canbe flooded with a sample to be processed.

According to various embodiments, the at least one capillary channel cancomprise an inner surface having a maximum inner cross-sectionaldimension, that can be, for example, a diameter. The capillary channelcan comprise a capillary tube. The capillary tube can have an innerdiameter of about 0.5 microns or less, about 1 micron or less, about 10microns or less, about 50 microns or less, about 100 microns or less,about 300 microns or less, or about 1000 microns or less, or greaterthan about 1000 microns. In various embodiments, the above dimensionscan refer to the maximal cross-sectional dimension of a capillarychannel that is not a capillary tube. Such a capillary channel can berectangular in shape or have another shaped deemed appropriate by one ofskill in the art. Various systems and apparati are provided that caninclude such a capillary channel.

According to various embodiments, the system can comprise at least onecapillary channel having a maximum inner cross-sectional dimension and asample preparation device. The sample preparation device can comprise,an aqueous sample injection unit in fluid communication with the atleast one capillary channel, and a spacing fluid injection unit in fluidcommunication with the at least one capillary channel. The aqueoussample injection unit and the spacing fluid injection unit can compriseseparate units each in fluid communication with the at least onecapillary channel, and a control unit adapted to flow an aqueous sampleand a spacing fluid from the aqueous sample injection unit and thespacing fluid injection unit, respectively, and adapted to injectvolumes of aqueous sample and spacing fluid that can respectively formslugs in the at least one capillary channel wherein each slug can havean outer dimension that is equal to the maximum inner cross-sectionaldimension. In various embodiments, the sample injection unit and thespacing fluid injection unit can comprise a single unit in communicationwith the at least one capillary channel. In various embodiments, thesystem can comprise a non-aqueous liquid source in fluid communicationwith the spacing fluid injection unit and an aqueous sample source influid communication with the aqueous sample injection unit.

According to various embodiments, the system can comprise a detectiondevice adapted to detect a component of the aqueous sample source or areaction product thereof. The detection device can comprise, forexample, a spectrophotometer or a fluorometer. Other detection devices,for example, a photomultiplier tube (PMT), photodiode, or charge-coupleddevice (CCD) can also be used.

According to various embodiments, the system can comprise at least onecapillary channel comprising an inner surface. The inner surface of theat least one capillary channel can comprise linker moieties. The linkermoieties can comprise at least one of steptavidin moieties or biotinmoieties. In various embodiments, the capillary channel can be acapillary tube.

According to various embodiments, the system can comprise a capillaryelectrophoretic sequencer adapted to inject a sample component when asample component is disposed on the electrically conductive surface. Thesample component, however, can be injected into a device other than anelectrophoretic sequencer, as deemed appropriate by one of skill in theart, or transferred into another system for further processing.

According to various embodiments, the electrically conductive surfacecan comprise channels. The channels can comprise linker moieties adaptedto bind to a nucleic acid.

According to various embodiments, the electrically conductive surfacecan comprise linker moieties adapted to bind to a nucleic acid. Thelinker moieties can comprise a plurality of the same linker moiety.

According to various embodiments a system is provided that can comprisean aqueous sample injection unit in fluid communication with at leastone capillary channel having a maximum inner cross-sectional dimension,a spacing fluid injection unit in fluid communication with the at leastone capillary channel, the aqueous sample injection unit and the spacingfluid injection unit can comprise separate units each in fluidcommunication with the at least one capillary channel. The system cancomprise an electrically conductive substrate and a capillaryelectrophoresis sequencer. In various embodiments, the system cancomprise, a control unit adapted to flow an aqueous sample and a spacingfluid from the aqueous sample injection unit and the spacing fluidinjection unit, respectively. The aqueous sample injection unit and thespacing fluid injection unit can be adapted to inject volumes of aqueoussample and spacing fluid to form slugs in the at least one capillarychannel wherein each slug has an outer dimension that is about equal tothe maximum inner cross-sectional dimension. In various embodiments, thesystem can comprise an electrically conductive substrate that cancomprise at least one channel and a capillary electrophoretic sequenceradapted to inject a sample component from the substrate when a samplecomponent is disposed on the electrically-conductive surface. Theelectrically conductive surface can comprise linker moieties adapted tobind to a nucleic acid. The linker moieties can comprise a plurality ofthe same linker moiety.

According to various embodiments, a method is provided. The method cancomprise, forming in a capillary channel a plurality of aqueous sampleslugs spaced apart from one another by slugs of spacing fluid, at leastone of the aqueous sample slugs comprising at least one target analyte,and dispensing the aqueous sample slugs one-at-a-time from the capillarychannel onto a substrate to form a pattern of spaced apart aqueoussamples on the substrate, the substrate comprising at least oneelectrically conductive surface that comprises at least one linkermoiety bound thereto, wherein the at least one linker moiety is adaptedto capture the at least one target analyte.

According to various embodiments, partitioned aqueous compartments canbe prepared for dispensing onto a substrate by methods other thanpreparing slugs in a capillary channel. Examples of preparations ofpartitioned sample can comprise forming aqueous compartmentalized samplein a non-constrained volume such as would be found in a capillarychannel or capillary tube. The compartments can be formed as a result ofemulsification as described, for example, by Ghadessy, et al., Proc.Natl. Acad. Sci. USA 98:45224557 (2001), which is incorporated in itsentirety herein by reference.

According to various embodiments, the method can comprise capturing theat least one target analyte with the at least one linker moiety to format least one captured target analyte. In various embodiments, the methodcan comprise contacting the electrically conductive surface with amixture of sequencing reaction components after capturing the at leastone target analyte.

According to various embodiments, the at least one electricallyconductive surface of the substrate can comprise a gold-coated surfaceor other metal-coated surfaces. In various embodiments, the at least onetarget analyte can comprise at least one target nucleic acid sequence.

According to various embodiments, the method can comprise reacting theat least one captured target analyte with a reagent mixture to form atleast one target analyte product. In various embodiments, the method cancomprise positioning a collection device adjacent the at least onetarget analyte product and injecting at least a portion of the at leastone target analyte product into the collection device. The collectiondevice can comprise a capillary of a capillary electrophoretic analyzer.

According to various embodiments, injecting in the method can compriseapplying a potential to the at least one electrically conductivesurface.

According to various embodiments, forming the pattern of spaced apartaqueous samples can comprise forming a plurality of rows of aqueoussamples.

According to various embodiments, a method is provided that can comprisemigrating components in a sample on a substrate surface into a capillarychannel, for example, a capillary tube. The components can be injected,for example, by electrokinetic force. Migration of the chargedcomponents can be accomplished by creating an electric field in a deviceor system. The system can comprise an electric field generator forproducing electrokinetic force. Conditions that can affectelectrokinetic injection of DNA samples, can comprise, sample ionicstrength, buffering capacity, the quality of the separation matrix beingused, the voltage, and the electrical field. Electrokinetic injectioncan rely on the application of an initial voltage through a passage toinitiate sufficient ion flow to bring the sample into the passage andthereafter producing electrophoretic separation conditions. A method ofelectrokinetic injection has been described in U.S. Pat. No. 6,569,305,issued May 27, 2003, which is incorporated in its entirety herein byreference.

According to various embodiments, a method is provided that can compriseforming in a capillary channel a plurality of aqueous sample slugs, atleast one of the aqueous sample slugs comprising at least one targetanalyte comprising at least one respective linkage group, and dispensingthe aqueous sample slugs one-at-a-time from the capillary channel onto asubstrate to form a pattern of aqueous samples on the substrate, thesubstrate comprising an electrically conductive surface adapted tocovalently bond the at least one respective linkage group to form anattached analyte.

According to various embodiments, the method can comprise covalentlybonding the at least one linkage group to the electrically conductivesurface to form at least one captured target analyte. In variousembodiments, the method can comprise contacting the electricallyconductive surface with a mixture of sequencing reaction componentsafter the covalently bonding. In other embodiments, the method cancomprise reacting the at least one captured target analyte with areagent mixture to form at least one target analyte product.

According to various embodiments, the method can comprise positioning acollection device adjacent the at least one target analyte product andinjecting at least a portion of the at least one target analyte productinto the collection device. The collection device can comprise acapillary of a capillary electrophoretic analyzer.

According to various embodiments, injecting in the method can compriseapplying a potential to the electrically conductive surface of thesubstrate. The electrically conductive surface can comprise agold-coated surface. In various embodiments, the at least one targetanalyte can comprise at least one target nucleic acid sequence. Invarious embodiments, forming the pattern of aqueous samples can compriseforming a plurality of rows of aqueous samples.

According to various embodiments, a method is provided that can compriseamplifying DNA in a plurality of aqueous sample slugs in a capillarychannel to form amplicons, each aqueous slug being separated from anadjacent aqueous slug by at least one oil slug, rastering or moving thecapillary channel comprising the amplicons over a substrate anddepositing the amplicons from the capillary channel onto the substrate,the substrate comprising an electrically conductive surface, attachingthe amplicons to the electrically conductive surface,

contacting the substrate with a sequencing reaction mixture to form atleast one dye-labeled spot, positioning a capillary of a capillaryelectrophoretic analyzer over the at least one dye-labeled spot,electrically contacting the dye-labeled spot with the capillary, andinjecting one or more components from the dye-labeled spot into thecapillary.

According to various embodiments, amplifying can comprise incorporatinga 5′-sulfhydryl group into a DNA molecule. In various embodiments, thesurface can comprise an electrically conductive surface. Theelectrically conductive surface can comprise a gold surface. In variousembodiments, the surface can comprise a binding moiety.

According to various embodiments, the method can comprise washing theelectrically conductive surface with a denaturing solution afterdepositing the amplicons from the capillary onto the electricallyconductive surface, in various embodiments, the sequencing reactionmixture can comprise a primer and a dye-labeled terminator and themethod comprises reacting the amplicons with the primer and thedye-labeled terminator to form the dye-labeled spot.

According to various embodiments, the method can comprise imaging theelectrically conductive surface and determining a location of thedye-labeled spot. In various embodiments, the method can compriseanalyzing the one or more components in the capillary electrophoreticanalyzer.

According to various embodiments, the electrically conductive surfaceused in the method can comprise reactive groups. The reactive groups cancomprise one or more of carboxy groups, amino groups, and hydroxylgroups.

According to various embodiments, the substrate can comprise a materialthat can be electrically conductive or can be a non-conductive materialcoated with an electrically conductive layer. The substrate cancomprise, for example, glass, plastics (for example, polypropylene,polystyrene, polycarbonante and mixtures thereof), inert materials orelectrically conductive metals. Electrically conductive metals cancomprise gold or platinum. If a substrate is not electricallyconductive, it can be coated with an electrically conductive coating.Electrically conductive coatings can comprise, for example, gold orplatinum. In various embodiments, electrically conductive metals cancomprise platinum group metals, for example, ruthenium, osmium,palladium, rhodium, and iridium (See U.S. Pat. No. 5,645,930 to Tsou etal., issued Jul. 8, 1997, which is incorporated herein in its entiretyby reference.)

In various embodiments, an electrically conductive substrate can becovered with an insulating material or dielectric material, for examplea plastic, and the combination of insulating material or dielectricmaterial with electrically conductive material can act as a capacitorwhen a potential is applied. When the potential is applied to thesubstrate covered with plastic, negative charged molecules can move intothe capillary, for example, a DNA molecule. In various embodiments,moieties can be attached to the non-conductive surface for binding tonucleic acids or other sample of interest.

According to various embodiments, a non-conductive substrate can becoated with a thin electrically conductive film, for example, a goldfilm.

Other methods of coating a surface with conductive films are known, forexample, production of nanoparticle thin films. See, Sastry, Pure Appl.Chem. 74:1621-1630 (2002), which is incorporated in its entirety hereinby reference. Example of films formed by layer-by layer nanoparticleassembly that can be driven by electrostatic interactions can comprise,for example, cationic and anionic polyelectrolytes as well as multilayerstructure comprising combinations of colloidal particles, for example,biomacro-molecules such as DNA. A gold film can be formed from a goldcolloidal solution.

Gold-coated substrates can be prepared, for example, by sputtering ananometer layer of chromium and gold onto a glass slide. Thiolated DNAcan then be attached to the gold-coated substrate. Additionalinformation concerning gold-coated substrates, thiolation of DNA, andother methods immobilizing DNA to a substrate can be found in Csáki, etal., Nucl. Acids Res. 29:No, 16 e81 (2001), Peelen, et al., Langmuir 21,266-271 (2005) which are incorporated in their entireties by referenceherein.

According to various embodiments, DNA can be amplified by a PCR.Starting material comprising, DNA fragments with primer sites A and Bcan be diluted, and PCR with primers A and B can be used to amplifysingle DNA fragments in aqueous solution (for example, in capillarieswith aqueous slugs separated by oil). Primer A (or forward primer) cancontain a 5′ sulfhydryl group Primer B (or reverse primer) can contain a5′ sulfhydryl group. The amplification can be performed in a system thatuses alternating partitioned portions, for example, spaced apart slugsof an aqueous solution comprising DNA and non-aqueous separating liquid,for example, an oil. In various embodiments, the sample can be preparedin bulk and then distributed or disposed onto a substrate for subsequentinjection into a device for further analysis or processing. Furtheranalysis can comprise analysis in a capillary electrophoresis device.

In some embodiments slugs containing both primer A and primer B can bedeposited on different spots, at least one spot of which reacts onlywith primer A and at least one spot of which reacts only with primer B.In some embodiments, two different slugs are provided with reactants foronly primer A or primer B and can be deposited on different locations onthe substrate that react with both primer A or primer B. In someembodiments, only primer A is included in or added to a first half ofthe slug while only primer B is included in or added to a separate,second half of the slug. A cycle sequencing reaction can then be carriedout on primers bound to the surface which can hybridize to a freefloating amplicon with an appropriate complimentary tail.

In some embodiments, a spot having an analyte bound thereto can becontacted with an injection fluid. The injection fluid can comprise anaqueous solution, low-salt buffer, for example, of micromolarconcentration. The injection fluid can facilitate injection of theanalyte into a capillary electrophoresis capillary. Once contacted withthe injection fluid, the bound analyte can be free from the surface byapplication of a relative potential between the surface an thecapillary.

Amplifying of a nucleic acid can comprise a thermal cycling nucleic acidsequence amplification process or an isothermal nucleic acid sequenceamplification process. If a thermal cycling nucleic acid sequenceamplification process is used, the process can comprise, for example, apolymerase chain reaction (PCR). The nucleic acid sequence amplificationreaction can comprise an exponential amplification process, for example,PCR, or a linear amplification process, as can occur during, forexample, during Sanger cycle sequencing. In various embodiments, othernucleic acid amplification processes can comprise, for example, ligasechain reaction (LCR), nucleic acid sequence based amplification (NASBA),Q-beta replicase (QB) amplification, or strand displacementamplification (SDA). These alternatives, as well as others known to oneskilled in the art can be used either by themselves or in combinationwith PCR to amplify nucleic acids, for example, in a multiplexedpreparation.

Nucleic acid sequence processing methods can comprise a first type ofnucleic acid amplification reaction followed by one or more of a seconddifferent type of amplification reaction, and/or detection assayreaction, can be carried out, for example, as described in U.S. PatentApplication No. 60/699,782 to Faulstich et al., filed Jul. 15, 2005,(Attorney Docket No. 5010-297), and in U.S. patent application Ser. No.11/487,729 to Faulstich et al., filed Jul. 17, 2006, which areincorporated herein in their entireties by reference.

After amplification or other nucleic acid manipulation, the capillarycan be rastered or otherwise moved across a gold surface, while thecontents of the capillary are pumped out. A “snail trail” can result inalternating aqueous and non-aqueous deposits on a substrate surface. Thesulfhydryl groups can form a linkage to a gold surface, therebyimmobilizing PCR amplicons to the surface wherever the capillary tip isplaced and a drop of aqueous solution is deposited. The speed of pumpingand the speed of rastering the capillary across the gold surface can beadjusted such that amplicons are appropriately spaced and do not mix.The speed can optionally be further modulated such that aqueous slugsare placed at intervals which correspond to spacing associated with acapillary electrophoresis instrument. Similarly, the rows can optionallybe spaced at intervals matching those of an electrophoresis instrument.A detector in combination with a controller can be used to insure thatthe aqueous slugs are properly spaced. In various embodiments, DNA canbe attached to the substrate or a material covering the substrate usinga linkages other than a thiol linkage, for example, abiotin-streptavidin linkage. Examples of methods for attaching a targetmolecule to a surface can be found, for example, in U.S. Pat. No.6,465,178 B2, issued Oct. 15, 2002, and U.S. Pat. No. 6,057,100, issuedMay 2, 2000 which are incorporated herein in their entireties byreference.

Once the amplicons have covalently attached to a surface, the surfacecan be washed under denaturing conditions in order to remove one strandof an amplicon duplex the non-sulfhydryl containing strand primed byprimer B, or primer A, as appropriate).

The surface can then be contacted with a sequencing mixture containingprimer B, and one round of standard dye-labeled terminator sequencingcan be performed. The surface is then washed under non-denaturingconditions to remove unreacted triphosphates and salts. The dye-labeledsequencing products remain hybridized to the template strands, which arecovalently bound to the gold surface. In some embodiments, a sequencingreaction can be carried out on the plate as described herein or theplate can be used for cleaning-up bound analytes.

Imaging of the electrically conductive surface, for example, a goldsurface, which can comprise DNA samples can be used to detect thelocation of each spot on the substrate containing labeled sequencingproducts. Detecting can be, for example, the result of fluorescentimaging of DNA containing a fluorescent label. In various embodiments, adetector can comprise photodiodes, photomultiplier tubes, orcharge-coupled device (CCD) cameras. The CCD camera can be, for example,an intensified CCD (ICCD). Examples of additional detectors and methodsfor labeling DNA, can be found in U.S. Pat. No. 6,255,083 B1, issuedJul. 3, 2003, which is incorporated in its entirety herein by reference.

After locating a spot comprising a labeled sequencing product, the endof a sequencing capillary can then positioned directly over a spot andthe sequencing product fragments solubilized, for example, by raisingthe temperature of the sequencing capillary enough to force a smallamount of polymer out of the end of the capillary to contact the goldsurface/sequencing products or by pumping a small amount of the polymerout of the end of the capillary, or by forming an aqueous bridge betweenthe gold surface/sequencing product and the sequencing capillary. Thenthe solubilized fragments are injected into the sequencing capillary byapplying a voltage across the gold surface. Without wishing to be heldto any specific theory of action, it is believed that surrounding spotsare not injected because 1) they are dry and/or 2) the only path ofelectrical conduction is through the capillary contact with the spot ofinterest.

According to various embodiments, the system can comprise a capillarychannel dimensioned so that a migration of charged components in afluid, from the substrate into the capillary can occur. The capillarychannel can have one or more maximum cross-sectional dimensions of about5 millimeters or less, for example, about 2 millimeters or less, about 1millimeter or less, or about 0.5 millimeter or less. In variousembodiments the capillary channel has an inner surface and a maximumdiameter of about 5 millimeter or less, for example, about 2 millimetersor less, about 1 millimeter or less, or about 0.5 millimeter or less anddimension is a diameter of a capillary tube. Other sizes can include 50microns, or, for example, from about 25 microns to about 75 microns.

While electrokinetic force can move a sample from the substrate into acapillary channel, this does not preclude the method from creating apressure differential between the sample on the substrate and thecapillary channel. Such a gradient and/or electrokinetic flow can play arole in migrating or moving the sample. According to variousembodiments, a pressure differential can be generated by activating apump.

The methods and systems can provide reductions in sequencing reagentconsumption. Assuming i) a standard 1 inch by 3 inch microscope slidecoated with gold, ii) aqueous slugs of 1 nl, iii) the aqueous phaseforms droplets on a gold surface with 90° contact angles, and iv) thesurface of the 1×3 inch slide can be covered with 1 ml of sequencingreaction liquid, the following exemplary calculation can be made,however, such calculation should in no way limit the scope of theclaims. Other formats, for example, a standard 96-well microtiter plateor the footprint thereof can be used as appropriate substrates.

A one nanoliter droplet can be calculated to form a spot with a diameterof 156 μm. Stearic interference can limit the packing density of doublestranded DNA to a diameter of about 2 nanometers. Taking a conservativepacking density of only one DNA per 20 nm², a 156 μm diameter featurecan be calculated to contain 9.6×10⁸ DNA molecules. Assuming asequencing reaction can generate termination products between +1 and+3,000 bp, each fragment size will contain on average 3×10⁵ molecules.If even 10% of these are electrokinetically injected, that can result in30,000 molecules per peak, which can be detected with current sequencinginstrumentation.

If a snail trail deposition is adjusted such that there are threediameters (468 micrometers) of blank space between amplicon features orspots, a 1×3 inch surface can hold 3,000 features. In other words, 3,000sequencing regions can be formed on a 1×3 inch “plate,” which uses 1 mlof sequencing reaction, or 0.3 μl per sequencing reaction. This canrepresent an order of magnitude reduction in sequencing reagentconsumption, thereby reducing the costs of such preparation.

The method and systems can provide high throughput shotgun sequencingprojects without the use of bacterial cloning, clone picking, plasmidpreparation, or microtiter plate-based sequencing reactions. The methodand systems can also provide high throughput preparations for geneticanalysis and/or other diagnostic methods using nucleic acids and/orrequiring multiple sampling of small volumes.

According to various embodiments, the method can involve the use of asystem or device that provides sample slugs to a substrate or capillarychannel, for further processing. The sample slugs can each comprise asingle target nucleic acid molecule or amplification product from asingle nucleic acid molecule or analysis, for example, in a solution ormixture. Further processing of the nucleic acid can comprise amplifyingthe nucleic acid and/or sequencing the nucleic acid. Further processingof molecules other than nucleic acids is also within the realm of thepresent teachings as will be appreciated by those of skill in the art.According to various embodiments, the slugs can either be flowedcontinuously or can be intermittently stationary in a capillary channelduring amplification and/or other procedures. Sample volumes comprisinga nucleic acid to be amplified or processed can be less than about 100μl, less than about 1 μl, less than about 500 nl, less than about 250nl, less than about 100 nl, less than about 50 nl, less than one nl,less than 100 pl, or less than 10 pl.

According to various embodiments, the sequencing methods that can becarried out using the devices and methods described herein and cancomprise direct sequencing, step-wise sequencing, Sanger sequencing,cycle sequencing, sequencing by synthesis, fluorescent in situsequencing (FISSEQ), sequencing by hybridization (SBH), forward/reversesequencing, pyrosequencing, sequencing using boronated oligonucleotides,electrophoretic, or microelectrophoretic sequencing, capillaryelectrophoretic sequencing, or other nucleic acid sequencing methodsknown in the art that can be applied to small sample volumes. Exemplarydescriptions of sequencing in various volumes can be found in U.S. Pat.No. 5,846,727 to Soper et al., U.S. Pat. No. 5,405,746 to Uhlen, U.S.Pat. No. 6,154,707 to Livak et al., and Soper et al., Anal. Chem.70:4036-4043 (1998), all of which are incorporated herein in theirentireties by reference.

According to various embodiments, the methods and systems can useTaqMan® reagents (Applied Biosystems, Cal.), for example, probes orprimers. For example, see U.S. Pat. No. 6,154,707 to Livak, et al.,incorporated herein in its entirety by reference. Other related methodsknown to one of skill in the art can also be used as deemed appropriate.Such reagents can be used in methods of analyzing DNA or RNA.

According to various embodiments, labeling of molecules can beaccomplished, for example, using an affinity labeled primer. Primers cancomprise an affinity moiety, thereby allowing for the binding ofreaction products to affinity-binding moieties. For example, a specificbinding pair comprising biotin and streptavidin can be employed. Abiotin affinity moiety can be incorporated into a primer, and astreptavidin binding moiety can be used to bind, or can bind andimmobilize the biotin-incorporated primer. Unbound unincorporatedreaction components can be removed, and the nucleic acid strandcomplementary to the biotin-bearing strand can be isolated and analyzed.It will be appreciated that the members of a specific binding pair canbe switched and still accomplish the desired binding to the surface ofthe substrate, for example, the streptavidin can be attached to theprimer and act as an affinity moiety, and the biotin can be attached toa solid support and act as a binding moiety. The procedures used forbinding, and/or binding and immobilization, are well known to one ofskill in the art. Bound, but unused single-stranded primer can be laterdigested.

According to various embodiments, a double-stranded amplicon with abinding moiety can be attached or immobilized to an inner surface of acapillary tube or other capillary channel. Various functional groups canbe used to accomplish attachment or immobilization of nucleic acids. Afunctional group can be any compound that can be incorporated into orattached to an oligonucleotide and that has a strong interaction to amolecule that can be immobilized on a solid-support. If elevatedreaction temperature is used to analyze or process an attached molecule,stability of the functional groups at such temperatures can be aconsideration.

According to various embodiments, samples of interest can be prepared ina capillary tube and then dispensed onto a substrate from which thesamples are electrokinetically injected into, for example, a capillaryelectrophoresis sequencing apparatus. In other embodiments, samples canbe directly processed in a capillary channel formed in an electricallyconductive substrate, thereby eliminating the dispensing step. Smallvolumes, for example, slugs can be used in such channels. Attached tothe surfaces of such channels can be binding moieties and/or specificnucleic acid sequences complimentary to a sample of interest. Once thesample of interest is bound to a location, the sample can then beinjected into, for example, a capillary electrophoresis apparatus forfurther analysis.

Examples of binding pairs can comprise biotin—avidin,biotin—streptavidin, or cystein-thiol groups. An example, of afunctional group for binding nucleic acids to a surface is11-biotin-dUTP. A biotin-avidin-biotin three component linkage of amolecule to be attached to a surface can also be used. If anoligonucleotide is attached to a surface, interaction between bindingcomponents on the surface and the oligonucleotide should be stableduring the amplification and/or other procedures. In variousembodiments, directly or indirectly, light activated or heat activatedreactive groups on a primer that can react with a surface coatedreactive group, can be used.

Incorporation of a terminal functional group into a nucleic acid beingsynthesized can be accomplished, for example, with a polymerase, such asKleno a T7, or reverse transcriptase. Alternatively, a functional groupof interest can be attached to an oligonucleotide by ligation to asuitable oligonucleotide that has already been synthesized.

According to various embodiments, the system can be used for carryingout sequence-specific nucleic acid reactions involving a target nucleicacid. Reaction-specific reagents can be releasably bound to the wall ofa capillary channel, for example, through duplex formation withimmobilized complimentary-sequence oligonucleotides, or by ligandattachment to an immobilized binding molecule. Complimentary sequenceoligonucleotides can comprise zip-code sequences or other sequences asdeemed appropriate by one of skill in the art.

According to various embodiments, methods and systems for microfluidicsample handling are provided. The methods can be used, for example, toperform shotgun sequencing, as well as other methods of nucleic acidanalysis. DNA to be sequenced can be prepared by standard techniques,for example, shearing of genomic DNA of interest. Primers can beattached to the two ends of the sheared DNA for further manipulation.

Nucleic acids for sequencing reactions can be prepared by methods knownto one of skill in the art. Methods can comprise chemical synthesis, orshotgun cloning in bacteria or yeast, as are well-known to those in theart. According to various embodiments, nucleic acids can also beprepared by enzymatic methods, for example, by a PCR reaction or a chainligase reaction. Enzymatic methods of amplification can provide analternative to the biological amplification of cloning in bacteria oryeast. Enzymatic amplification can provide sufficient DNA for micro- ornano-sequencing reactions.

According to various embodiments, an amplicon can be obtained in anaqueous slug by the described methods. Amplification of target nucleicacids, with detection resulting from the increased amount of targetrelative to the copy number present in the starting material, can beaccomplished. Suitable amplification procedures can include thepolymerase chain reaction, and isothermal amplification, although itwill be appreciated that other amplification strategies might beemployed in order to generate product.

According to various embodiments, an enzyme that polymerizes nucleotidetriphosphates into amplified fragments can be a heat-resistant DNApolymerase. Polymerases that can be used in a method of the presentteachings comprise DNA polymerases from such organisms as Thermusaquaticus, Thermus thermophilus, Thermococcus litorails, Bacillusstearothermophilus, Thermotoga maritimia and Pyrococcus ssp. The enzymecan be isolated from source bacteria, produced by recombinant DNAtechnology or purchased from commercial sources. Exemplary DNApolymerases that can be used include those available from AppliedBiosystems (Foster City, Calif.), for example, AmpliTaq Gold™ DNApolymerase; AmpliTaq™ DNA Polymerase; Stoffel fragment; rTth DNAPolymerase; and rTth DNA Polymerase XL. Other suitable polymerases thatcan be used include, but are not limited to, Tne, Bst DNA polymeraselarge fragment from Bacillus stearothermophilus, Vent and Vent Exo—fromThermococcus litoralis, Tma from Thermotoga maritima, Deep Vent and DeepVent Exo—and Pfu from Pyrococcus, and mutants, variants and derivativesof the foregoing. For further discussion of polymerases, and applicablemolecular biology procedures generally, see, Ausubel et al., CurrentProtocols in Molecular Biology, John Wiley & Sons, New York, 2001, andThe Polymerase Chain Reaction, Mullis, K. B., F. Ferre, and R. A.,Gibbs, Eds., Molecular Cloning: A Laboratory Manual, (3rd ed.) Sambrook,J. & D. Russell, Eds. Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. (2001), all of which are incorporated herein in theirentireties by reference.

Amplification reaction times, temperatures, and cycle numbers can bevaried to optimize a particular reaction. Addition of additives toreduce stutter and reduce non-specific amplification can also be used asdetermined appropriate by one of skill in the art, for example, see USPatent Application Publication 2005/0112591 to Dimoski et al., which isincorporated herein in its entirety by reference.

According to various embodiments, a DNA library can be prepared foranalysis. Genomic libraries have been prepared by a variety of methods,for example, restriction digestion and ligation, mechanicalfragmentation and enzymatic “tailing,” and PCR amplification usingprimers, however, libraries other than genomic libraries can also beprepared. Methods of library preparation are known in the art, forexample, in Nucl. Acids Res. 25:781-786 (1997), Nucl. Acids Res.17:3645-3653 (1989), both of which are incorporated herein in theirentireties by reference.

A library can be prepared enzymatically without first cloning DNA inbacteria. DNA can be digested or sheared into appropriate sizedfragments, for example, fragments of about 50 bp, 100 bp, about 200 bp,about 500 bp, about 1000, or about 2000 bp. Sheared DNA can be filled inby 5′ phosphorylation or polymerization using a Klenow fragment of DNApolymerase, for example, see Kinzler et al., Nucleic Acids Res.17:3645-3653 (1989), incorporated herein by reference, and adapters canthen be ligated to ends of sized fragments for attachment to anappropriate surface. An adapter can comprise a sequence of interestattached to a biotin moiety that has been ligated to a DNA fragment. Thebiotin moiety permits a DNA fragment to bind to a surface, for example,a bead or a capillary channel coated with streptavidin. Other bindingmethods can be used as well, for example, peptide nucleic acid, lockednucleic acid, and LDNA binding methods.

According to various embodiments, biotin-streptavidin can be a suitablechoice for attaching a nucleic acid to a surface for generation of anucleic acid library, as well as for amplification and sequencingreactions in a capillary channel, because a biotin-streptavidin linkagecan withstand large and rapid temperature changes experienced inperforming such reactions. Attachment by other than abiotin-streptavidin linker can also be used. Such tinkers should also beable to withstand large and rapid temperature changes. If, however, anisothermal method is used, stability to large and rapid temperaturechanges may not be necessary.

If an oligonucleotide is to be attached to a substrate, the attachmentcan be done either batch-wise with a substance-coupled carrier slurriedin a suitable medium, or on a column comprising an activated carrier.Any conventional carrier material (for example, Sepharose beads,(Pharmacia, Sweden)), filters, capillaries, or plastic dipsticks (forexample, polystyrene strips), and microtitre wells to which thesubstance can be sufficiently coupled, can be used, depending on theapplication for which a nucleic acid is to be used.

Unfilled portions of a DNA fragment can be filled in and the complementcan be displaced by denaturation. Fragments of interest can be collectedand quantitated. A collected fragment can include, for example, variableregions of genomic DNA.

According to various embodiments, nucleic acids generated by a library,can be diluted by a limiting dilution procedure such that aconcentration of a single molecule of interest per a given volume ofliquid can be obtained. Nucleic acids obtained by any method can bediluted to a concentration of about one molecule per given volume priorto analysis. When a sample is diluted to this extent, some volumes maynot have any nucleic acid molecules, while others can have more than 1molecule. For example, in some embodiments, a plurality of volumes, canhave a single molecule. In other embodiments, about 10% or less, about20% or less, about 30% or less, or about 50% or less of the volumes canhave a single molecule. One of skill in the art can appreciate how toprepare a solution by limiting dilution. After a sample is diluted bylimiting dilution, a single nucleic acid molecule can be introduced intoa capillary channel in an aqueous slug. Not all aqueous slugs formedfrom a nucleic acid solution theoretically diluted to one molecule pergiven volume will necessarily have a nucleic acid in every given volume.In various embodiments, about 10% or less, about 20% or less, about 30%or less, about 40% or less, about 50% or less, about 60% or less, about70% or less, about 80% or less, about 90% or less, about 95% or less, orabout 99% or less, of the aqueous slugs can have one nucleic acidmolecule per given volume. In various embodiments, at least about 1% ormore, about 5% or more, about 10% or more, or about 20% or more of theaqueous slugs can have one nucleic acid molecule per given volume.

According to various embodiments, a set of immiscible fluid discretevolumes of an aqueous liquid spaced-apart from one another by animmiscible spacing fluid can be prepared in a conduit. According tovarious embodiments, the conduit can comprise, for example, a capillarychannel, a tube, a groove, or a channel formed by opposing barriers.

According to various embodiments, PCR can be performed in an aqueousdiscrete volume in a conduit to amplify a nucleic acid molecule,although other methods can be used to amplify the nucleic acid molecule,for example, reverse transcriptase PCR (RT-PCR) or a ligase chainreaction. During amplification, a terminal moiety comprising, forexample, a caged biotin, can be incorporated into the nucleic acid beingsynthesized or amplified such that an amplified nucleic acid (amplicon)can be treated to attach the nucleic acid to an inner surface of acapillary channel. The terminal moiety can be incorporated throughprimer used in amplification. In some embodiments, the terminal moietycan be located at a position other than the 3′ or 5′ termini of thepolynucleotide of interest provided that the moiety can be used toattach the amplicon to a solid support. According to variousembodiments, a single DNA molecule can be attached first to an innersurface in a conduit and then amplified. In other embodiments, the DNAbeing amplified need not be attached to the inner surface of theconduit. Rather, the DNA is amplified in the discrete volume, eitherduring movement through the conduit or when the conduit in maintained ina stationary position in or on a thermal cycling device. The amplifiedsample can be dispensed onto the electrically conductive substrate afteramplification in the aqueous slugs.

The system can comprise a thermal cycling device. The thermal cyclingdevice can, for example, be adapted to thermally cycle an aqueous sampleor the electrically conductive substrate. The thermal cycling device cancomprise a heat source, for example, a radiant or non-radiant heatsource, and a cooling source, for example, a fan, an air jet, or aliquid-circulating system in a thermal block. The thermal cycling devicecan comprise one or more temperature sensors and one or more controlunits for controlling heating and cooling according to a desired thermalcycle. The thermal cycling device can be in direct contact with thesample or surface to be thermally controlled, but does not necessarilyneed to do so.

According to various embodiments, compartmentalized target nucleic acidscan be amplified from an initial single copy to a number of copiessuitable for downstream sequencing reactions. Amplification of DNA canbe accomplished by a number of methods, including but not limited to,polymerase chain reaction, rolling circle amplification or multiplestand displacement. The amplified DNA can then be injected from anelectrically conductive surface into a capillary channel.

The apparatus can be part of an integrated system and/or be adapted tofunction with other pieces of equipment adapted for further sampleprocessing of samples, for example, an ABI 310, ABI 3130, ABI 3130xl,ABI 3700, ABI 3730, or ABI 3730xl capillary electrophoretic analyzer(available from Applied Biosystems, Foster City, Calif.) that can beused for sequencing. In some embodiments, the apparatus can be part ofan integrated system and/or be adapted to function with other pieces ofequipment adapted for further sample processing of samples, for example,a PCR detector. Exemplary detectors that can be used include real-timesequence detection systems and real-time PCR detectors, for example, theABI 7900, available from Applied Biosystems, Foster City, Calif. Invarious embodiments, the apparatus provided can be used as a back-endsample deposition device.

The apparatus, system and/or methods described herein can also be usedin conjunction with downstream processing ofimmiscible-fluid-discrete-volumes in conduits as described, for example,in FIGS. 10 and 11 of U.S. Provisional Patent Application No. 60/710,167entitled “Sample Preparation for Sequencing” to Lee et al., filed Aug.22, 2005 (Attorney Docket No 5841P), or U.S. Provisional PatentApplication No. 60/731,133 entitled “Method and System for Spot Loadinga Sample” to Schroeder et al., filed Oct. 28, 2005 (Attorney Docket No.5010-288) which applications are incorporated herein in their entiretiesby reference. If there is any discrepancy between the description ofimmiscible-fluid-discrete-volumes in an immiscible fluid in the aboveprovisional applications and this one, this application is deemed to becorrect.

While the present teachings primarily relate to processing a discretevolume after it has been generated and processed, an entire system andmethod is provided, according to various embodiments, that compriseseither or both of generating and processing animmiscible-fluid-discrete-volume. An exemplary system and method isdescribed and shown in connection with FIGS. 1A and 1B herein.

FIGS. 1A and 1B are the left-side and right-side, respectively, of aschematic diagram detailing an example of a fluid processing system 10for processing fluid immiscible-fluid-discrete-volumes. The six conduitson the right-hand side of FIG. 1A and terminating in arrow headspointing to the right are respectively continued as the six conduitsshown on the left-hand side of FIG. 1B and terminating in arrow headspointing to the left, such that the top conduit of each respective sixdepicted are continuations of each other, and so on going down thefigures.

Generally, system 10 can be configured to perform different types ofassays on fluids introduced thereinto. The amounts and types of fluidsintroduced into system 10 can be varied depending on a particular assayto be performed. Exemplary assays can include, for example, de novonucleic acid sequencing reactions, and nucleic acid resequencingreactions, as discussed herein. An exemplary type of sample preparationcan be used for genotyping, gene-expression, methylation analysis,and/or directed medical sequencing (VariantSEQr™, for example, anApplied Biosystems product comprising primers for resequencing genes anddetecting variations) that requires multiple liquids to be broughttogether in an aqueous discrete volume. For example, in agene-expression application, each aqueous discrete volume can containindividual primer sets. The sample to be analyzed, for example,complementary DNA (cDNA), can be added to each aqueous discrete volume.In the VariantSEQr™ application, for example, an aqueous discrete volumecan comprise a primer set, and genomic DNA can be added to that discretevolume.

According to various embodiments, one or more sample fluids 22, 24, canbe introduced to system 10. Sample fluids 22 and 24, for example, cancomprise a nucleic-acid-containing fluid. According to some embodiments,the nucleic acid contained in a sample fluid can be, for example, asingle copy of a genomic DNA sequence of an organism, or complementaryDNA from an organism.

In some embodiments, a plurality of fluids can be introduced into fluidprocessing system 10 by way of animmiscible-fluid-discrete-volume-forming conduit 12, which is a part ofmain conduit system 50. Suitableimmiscible-fluid-discrete-volume-forming conduits include, for example,pipettes, capillaries, electro-wetting capillaries, needles, and anydevice configured to be in fluid communication with fluid processingsystem 10. Immiscible-fluid-discrete-volume-forming conduit 12 can bepart of a system that can comprise, for example, a pump or anotherapparatus adapted to produce controlled intake of fluids through intaketip 13 into immiscible-fluid-discrete-volume-forming conduit 12. Theimmiscible-fluid-discrete-volume-forming conduit 12 can be adapted tocontrol an introduction unit to introduce alternate volumes of aqueoussample fluid and spacing fluid that together form discrete volumes ofaqueous sample fluid in contact with spacing fluid, i.e., aqueous sampleimmiscible-fluid-discrete-volumes, in the at least one conduit whereineach aqueous sample immiscible-fluid-discrete-volume can comprise amaximum outer dimension that is equal to or slightly less than themaximum inner cross-sectional dimension ofimmiscible-fluid-discrete-volume-forming conduit 12. One of skill in theart will understand that the maximum inner cross-sectional dimension ofa conduit is the inner diameter of the conduit if the conduit has acircular cross-section.

According to various embodiments,immiscible-fluid-discrete-volume-forming conduit 12 can comprise a tip13. Tip 13 can interface with fluids to be drawn into system 10. Tip 13can comprise an angled surface or have any suitable geometry such thatthe creation of air bubbles in immiscible-fluid-discrete-volume-formingconduit 12 is minimized or eliminated when tip 13 contacts and draws ina fluid. A detailed description of tip 13 can be found below in thedescription of FIG. 13. Immiscible-fluid-discrete-volume-forming conduit12 can be robotically controlled, or manually controlled. Roboticconfigurations can comprise, for example, stepper motors 14, 16, and 18,which can move immiscible-fluid-discrete-volume-forming conduit 12 inX-axis, Y-axis, and Z-axis directions, respectively. In someembodiments, tube 12 can be moved in the Z-axis direction by a steppermotor 18, and a fluid container can be moved in the X-axis and Y-axisdirections by stepper motors 14 and 16, respectively. In someembodiments, tube 12 can be stationary and a fluid container can bemoved in the X-axis, Y-axis, and Z-axis directions by stepper motors 14,16, and 19, respectively. Motive force providers other than steppermotors can be used.

According to various embodiments, a variety of fluids can be introducedinto fluid processing system 10, in a number of different combinations,depending on the particular type of assay to be performed. The fluidscan reside on any suitable fluid retaining device, for example, in thewells of a multi-well plate 20, an opto-electrowetting plate, a tube ofpreformed slugs, a tube of stable emulsified nanodroplets, individualtubes, strips of tubes, vials, flexible bags, and the like.

According to some embodiments, fluid processing system 10 can comprise anumber of different fluid conduits and fluid control devices. Thefollowing description applies to the embodiment as illustrated in FIGS.1A and 1B, but one skilled in the art will understand that alterationsto fluid processing system 10 can be made while the teachings remainwithin the scope of the present teachings. As illustrated, fluidprocessing system 10 can comprise a main system conduit 50. Main conduitsystem 50 can comprise a plurality of conduits each in fluidcommunication with, for example, the following exemplary components:T-junctions 52, 66, and 84; holding conduits 56, 60, 63, 64 and 65;valves V-1, V-2, V-5, V-6, V-7, V-8, V-9, V-10, V-11, V-12, and V-13;cross-junctions 68, 70, 76, 86, and 88; and thermal spirals 74, 80, 90,and 92. Along conduit 50, thermal spirals 74, 80, 90, and 92 can be inthermal contact with respective thermal cyclers 74A, 80A, 90A and 92AEach thermal cycler 74A, 80A, 90A, and 92A can independently comprise aliquid bath, an oven, a plate, a block comprising fluid passagestherein, a peltier device, or the like thermal cycling device.

Main conduit system 50 can provide a fluid communication betweenT-junction 52 and output conduit 54. From T-junction 52, conduit system50 comprises two pathways that join at cross-junction 68. A firstpathway can take a fluid sequentially through holding conduits 56, 60and 64, and T-junction 66, before reaching cross-junction 68. A secondpathway can take a fluid sequentially through holding conduits 50, and65, and through either T-junction 66, to cross-junction 68, or directlyto cross-junction 68. Both the first pathway and the second pathways areconfigured to hold fluids for later analysis and are configured tointerface with devices for moving fluids along the conduits as discussedbelow.

From cross-junction 70, fluids can move sequentially to thermal spiral74, cross-junction 76, thermal spiral 80, and T-junction 84. AtT-junction 84 fluids can sequentially move either through cross-junction86, thermal spiral 90, and output conduit 54, or through cross-junction88, thermal spiral 92, and an output conduit.

According to some embodiments, fluid processing system 10 can comprisepumps 39 and 40. Pump 40 can be configured to remove or add oil to mainconduit system 50, and thereby move fluids located therein. Pump 39 canbe configured to remove or add oil to main conduit system 50 to movefluids located therein. All of the pumps described herein can createpositive and/or negative pressures in the various conduits of system 10.

According to various embodiments, a T-junction can comprise any junctionhaving three discrete pathways extending from, for example, either aY-junction or a T-junction. In various embodiments, the junction cancomprise a valve-less junction where a stream of aqueous sample fluidand a stream of non-aqueous spacing fluid can meet and form at leastdiscrete volumes of the aqueous sample fluid in contact with thenon-aqueous spacing fluid. For example, microfabrication technology andthe application of electrokinetics or magnetohydrodyamics can achievefluid pumping in valve-less, electronically controlled systems.Components comprising shape-optimized conduit turns, optimalintroduction methods, micromixers, and/or high flow rate electroosmoticpumps can be used in such a valve-less system.

According to some embodiments, system 10 can comprise discrete volumedetectors D-1, D-2, D-3, D-4, D-5, D-6, D-7, D-8, D-9, D-10, D-11, D-12,D-13, D-14, D-15, D-16, D-17, D-18, D-19, and D-20, and detector 98. Thediscrete volume detectors can comprise, for example, fluorescentdetectors, infra-red detectors, capacitive detectors, absorptiondetectors, refractive-index detectors, combinations thereof, and thelike. In FIGS. 1A and 1B, all of the detectors depicted are infra-red,refractive-index detectors with the exception of detector 98 which is afluorescent signal detector, although other arrangements can be used.The discrete volume detectors can be configured to distinguishimmiscible-fluid, discrete volumes from spacing fluid or oil as thediscrete volumes travel through the conduits of system 10.

According to various embodiments, the system can comprise athermal-cycling device or thermal cycler, adapted to thermally cycle anaqueous immiscible-fluid, discrete volume in a conduit disposed thereonor therein. In some embodiments, the conduit can contact the thermalcycler in a single straight-line segment, or a coil around the externalperimeter of thermal cycler, or a spiral of decreasing radius on onesurface, or a serpentine pattern across one or more surfaces of thermalcycler. The thermal-cycling device can comprise a heat source, forexample, a radiant heat source, a non-radiant heat source, a peltierdevice, or the like, and a cooling source, for example, a fan, an airjet, or a liquid-circulating system in a thermal block. Thethermal-cycling device can comprise one or more temperature sensors andone or more control units for controlling heating and cooling accordingto a desired or programmed thermal cycle.

In some embodiments, the conduits of the present teachings can comprisecapillary tubes having an inner diameter and the inner diameter can be,for example, about 1000 microns or less, for example, about 800 micronsor less, or about 500 microns or less. In some embodiments, the conduithas a minimum inner dimension, or diameter, of from about 1.0 micron toabout 100 microns, or from about 50 microns to about 75 microns. Inother embodiments, the conduit can have an inner diameter greater thanabout 300 microns. In some embodiments, the conduit can comprise aninner diameter in the range of from about 0.015 inch to about 0.025inch, for example, from about 0.019 inch to about 0.025 inch. In someembodiments, the conduit can have a smaller diameter at and/or beginningbefore a pair of thermal spirals near the downstream end of the systemwhich are designed for forward/reverse sequencing amplification. Otherdetails about the thermal-cycling device, capillary channel or conduit,and other system components will become apparent in view of theteachings herein.

System 10 can comprise a single molecule amplification fluid (“SMAF”)conduit system 51. SMAF tube system 51 can supply sample fluid to aT-junction through positive pressure rather than by aspiration. SMAFconduit system 51 can comprise a supply conduit connected to and influid communication with a supply of single molecule amplificationfluid. The SMAF can comprise a solution or mixture of target nucleicacids diluted to a degree such that there is an average of less thanabout one target nucleic acid per volume of single moleculeamplification fluid that is used to make animmiscible-fluid-discrete-volume. An exemplary concentration of targetmolecules can be 0.4 molecule per volume used to make animmiscible-fluid-discrete-volume. SMAF conduit system 51 can compriseconduits connecting a SMAF reservoir 69 sequentially to valve V-18 andT-junction 67. SAMF conduit system 51 can comprise conduits that connectT-junction 67 to main conduit system 50 and a rotary valve 71.

Fluid processing system 10 can comprise rotary valves 71, 73, 75, 77,and 79. Each rotary valve can function to direct the flow of meteredamounts of different reagents from different respective reagentreservoirs connected thereto, as described below, to main conduit system50. Syringe pumps 58, 66, 78, and 82 can be in fluid communication withrotary valves 73, 75, 77, and 79, respectively. Pumps 42, 43, 44, and 45can be in fluid communication with rotary valves 73, 75, 77, and 79,respectively.

Fluid processing system 10 can comprise a first waste conduit system 81.Waste conduit system 81 can comprise conduits connecting the followingcomponents: valves V-17, V-20, V-21, V-22, V-23, V-24, V-25, and a wastereservoir 83. Waste conduit system 81 can provide a fluid communicationbetween and cross-junctions 68, 70, 76, 86, and 88 and waste reservoir83.

Fluid processing system 10 can comprise a second waste conduit system48. Second waste conduit system 48 can comprise conduits connecting apump 87, a waste reservoir 85, and a valve V-26, that interface withoutput conduit 54. Second waste conduit system 48 can be used to removeliquids from output conduit 54.

Fluid processing system 10 can comprise reagent reservoirs 89, 91, 93,95, 97, and 99 and can be in fluid communication with rotary valves 75,77, 77, 79, 79, and 73, respectively. Reagent reservoir 89 can contain,for example, an exonuclease and shrimp alkaline phosphatase. Reagentreservoir 91 can contain, for example, nucleic acid amplificationreaction forward primers. Reagent reservoir 93 can contain, for example,nucleic acid amplification reaction chain terminating dyes. Reagentreservoir 95 can contain, for example, nucleic acid amplificationreaction reverse primers. Reagent reservoir 97 can contain, for example,nucleic acid amplification reaction chain terminating dyes. Reagentreservoir 99 can contain, for example, a nucleic acid amplificationreaction master mix comprising, for example, reactive single basenucleotides, buffer, a polymerase, and the like, for example, to carryout a polymerase chain reaction.

According to various embodiments, fluid processing system 10 cancomprise a rinse conduit system 30. Rinse conduit system 30 can providea fluid communication between a rinse fluid reservoir 28, rotary valve73, rotary valve 75, and immiscible-fluid-discrete-volume-formingconduit 12. Rinse fluid reservoir 28 can contain a rinse fluid 26. Rinsefluid 26 can comprise microbiologic grade water, for example, distilled,de-ionized water:

Rinse fluid 26 can be used to remove residual sample, for example, fromimmiscible-fluid-discrete-volume-forming conduit 12. Rinse fluid can beprovided to multi-well plate 20, by way of rinse conduit system 30.Rinse fluid 26 can be used as a rinse at the input station, and/or canbe used as a rinse fluid, a dilution fluid, or both, elsewhere in thesystem. In some embodiments, rinse fluid 26 can be added toimmiscible-fluid, discrete volumes to adjust the volume or concentrationthereof, in conjunction with an addition station, as described in FIG.1C.

According to various embodiments, fluid processing system 10 cancomprise a spacing fluid conduit system 36. Spacing fluid conduit system36 can provide a fluid communication between a spacing fluid reservoir34, vacuum pump 41, and multi-well plate 20. Spacing fluid reservoir 34can contain an oil 32 or other spacing fluid that is immiscible with animmiscible-fluid-discrete-volume-forming fluid, for example, an aqueousslug fluid.

In some embodiments, the spacing fluid can be non-aqueous. The spacingfluid can comprise an organic phase, for example, a polydimethylsiloxaneoil, a mineral oil (e.g., a light white mineral oil), a silicon oil, ahydrocarbon oil (e.g., decane), a fluorinated fluid or a combinationthereof.

Fluorinated compounds such as, for example, perfluoroooctyl bromide,perfluorodecalin, perfluoro-1,2-dimethylcyclohexane, FC 87, FC 72, FC84, FC 77, FC 3255, FC 3283, FC 40, FC 43, FC 70, FC 5312 (all “FC”compounds are available from 3M, St. Paul, Minn.), the Novec® line ofHFE compounds (also available from 3M, St. Paul, Minn.), such as, forexample, HFE-7000, HFE-7100, HFE-7200, HFE-7500, andperfluorooctylethane can also be used as the spacing fluid.Combinations, mixtures, and solutions of the above materials can also beused as the spacing fluid.

In some embodiments, fluorinated alcohols, such as, for example, 1H, 1H,2H, 2H-perfluoro-decan-1-ol, 1H, 1H, 2H, 2H-perfluoro-octan-1-ol, and1H, 1H-perfluoro-1-nonanol can be added to a fluorinated compound, suchas those listed above, to improve the stability of aqueous discretevolumes within the spacing fluid, but still maintain the ability tocoalesce upon contact. In some embodiments, fluorinated alcohols can beadded in a range of approximately 0.1% to approximately 5% by weight. Insome embodiments, the fluorinated alcohol additive can be approximately0.1% 0.2%, 0.5%, 1.0%, 1.5%, 2.0%, 3.0%, 4.0% or 5% by weight of thefluorinated compound. In some embodiments, the fluorinated alcoholadditive can be from approximately 1% to approximately 10% by volume ofthe fluorinated compound. In some embodiments, the fluorinated alcoholadditive may comprise approximately 1%, 2%, 4%, 5%, 6%, 7%, 8%, 9%, or10% by volume of the spacing fluid. In some embodiments, F-alkyldimorpholinophosphates can be added as surfactants to fluorinatedcompounds.

In some embodiments, the organic phase can include non ionic surfactantssuch as sorbitan monooleate (Span 80 (no. S-6760, Sigma)),polyoxyethylenesorbitan monooleate (Tween 80 (no, S-8074, Sigma)),sorbitan monostearate (Span 60), octylphenoxyethoxyethanol (Triton X-100(no. 19284, Sigma)). In some embodiments, Span 80 can be added in anamount ranging from about 1.0% to about 5.0%, or about 3.0% to about4.5%. In some embodiments, adding surfactants in the quantities of 4.5%Span 80, 0.40% Tween 80, and 0.05% Triton X-100 to mineral (no. M-3516,Sigma) can result in the creation of stable emulsified droplets.

In some embodiments, the organic phase can include ionic surfactants,such as sodium deoxycholate, sodium cholate, and sodium taurocholate. Insome embodiments, the organic phase can include chemically inertsilicone-based surfactants, such as, for example,polysiloxane-polycetyl-polyethylene glycol copolymer. In someembodiments, the non-aqueous, spacing fluid can have a viscosity betweenapproximately 0.5 to approximately 0.75 centistokes. In someembodiments, the non-aqueous spacing fluid can have a viscosity betweenapproximately 0.75 centistokes to about 2.0 centistokes. In someembodiments, the non-aqueous spacing fluid can have a viscosity greaterthan 2.0 centistokes. In some embodiments, the non-aqueous spacing fluidcan have a viscosity between 0.5 to greater than about 2.0 centistokes.In some embodiments, the non-aqueous spacing fluid can have a viscositygreater than 2.0 centistokes, in some embodiments, the non-aqueous,spacing fluid can have a boiling point greater than or equal to 100° C.

Spacing fluid 32 can function to separate discrete volumes of animmiscible-fluid-discrete-volume-forming fluid, for example, and aqueoussample, before, during, or after theimmiscible-fluid-discrete-volume-forming fluid has s been introducedinto system 10. Spacing fluid can be provided to multi-well plate 20,from a spacing fluid reservoir 34, by way of a spacing fluid conduitsystem 36.

According to some embodiments, a de novo nucleic acid sequencing methodis provided that uses system 10. The de novo sequencing method can beused to sequence an entire genome or portions thereof. The de novosequencing method can be especially useful when the sequence of theorganism is unknown.

In some embodiments, a de novo sequencing method comprisespre-processing a sample, separating the sample into a set ofimmiscible-fluid, discrete volumes, optionally adding amplificationreagents to each discrete volume of the set, amplifying nucleic acids inthe set of immiscible-fluid, discrete volumes to form a set of amplifiedimmiscible-fluid, discrete volumes, optionally detecting, and removing,discrete volumes without amplified sample molecules therein, addingprimer and dNTP deactivation agents to each discrete volume in the set,or optionally, to only those with amplified sample molecules, incubatingthe set of amplified immiscible-fluid, discrete volumes with primer anddNTP deactivation agents, subjecting the resulting nucleic acids tosequencing conditions to form detectable products, and detecting thedetectable products.

In some embodiments, the method can comprise pre-processing a samplebefore the sample fluid is introduced into system 10. The pre-processingof a sample can comprise fragmenting the nucleic acid present in thesample fluid. The fragmentation can be accomplished by any suitablemethod known in the art. For example, the nucleic acid can be fragmentedby enzymatic digestion, or physical disruption methods, for example,hydro-sheering or sonication. In some embodiments the nucleic acid canbe fragmented to an average size of about 500 B, 750 B, 850 B, 1 KB, 2KB, or 3 KB, for example.

According to some embodiments, the pre-processing of sample can compriseligating sequences to a sample. Universal sequences can be used tofacilitate universal nucleic acid amplification. Universal sequences canbe artificial sequences that generally have no homology with the targetnucleic acids. Universal sequences can be designed to resist theformation of dimers between themselves. Universal sequences can bedesigned to bind with analogous primers with a consistent efficiency.

According to some embodiments, the present teachings can encompass a denovo sequencing method wherein universal sequences can be ligated to the5′ and 3′ ends of the DNA fragments in a sample by, for example, T4 DNAligase, thereby forming a universal tail. The universal tail sequencescan function as sites of complementarity for zip code primers. Detailsof universal tail procedures can be found in U.S. Pat. App. No.2004/0185484, to Costa et al., which is incorporated herein, in itsentirety, by reference.

According to various embodiments, the amplifying of a nucleic acid cancomprise a thermal cycling nucleic acid sequence amplification processor an isothermal nucleic acid sequence amplification process. If athermal cycling nucleic acid sequence amplification process is used, theprocess can comprise, for example, a polymerase chain reaction (PCR).The nucleic acid sequence amplification reaction can comprise anexponential amplification process, for example, PCR, or a linearamplification process, as can occur during, for example, during Sangercycle sequencing. In various embodiments, other nucleic acidamplification processes can be used, for example, ligase chain reaction(LCR), nucleic acid sequence based amplification (NASBA), Q-betareplicase (QB) amplification, or strand displacement amplification(SDA). These alternatives, as well as others known to one skilled in theart, can be used either by themselves or in combination with PCR toamplify nucleic acids.

According to various embodiments, nucleic acid sequence processingmethods comprising a first type of nucleic acid amplification reactionfollowed by one or more of a second different type of amplificationreaction, and/or detection assay reaction, can be carried out, forexample, as described in U.S. Patent Application No. 60/699,782 toFaulstich et al., filed Jul. 15, 2005, and in U.S. patent applicationSer. No. 11/487,729 to Faulstich et al., filed Jul. 17, 2006, which areincorporated herein in their entireties by reference.

According to some embodiments, the present teaching can comprise amethod of de novo sequencing wherein pre-processing of sample cancomprise adding zip code primers to a sample of nucleic acid havinguniversal tail sequences ligated therein. Zip code primers can becomplementary to the universal tail sequences. The use of zip code tailssequences and zip code primers can reduce the need for target specificprimers, resulting in significant cost savings as well as greater assayflexibility.

According to various embodiments, pre-processing a sample can compriseadding to the sample reactants to facilitate a nucleic acidamplification reaction. For example, the four dNTP's (dATP, dTTP, dGTP,and dCTP), a polymerase, oligonucleotide primers, and/or chelatingagents can be added to the sample. Oligonucleotide primers can be chosenas determined by one of skill in the art to accomplish the desiredobjective, for example, universal primers can be used.

According to various embodiments, pre-processing a sample can comprisediluting the sample with a miscible solvent, vehicle, or carrier. Thesample can be diluted at a ratio of 1:1, 1:10, 1:100, 1:1000, or1:10,000, for example. Exemplary ranges of dilution can be from about1:1 to about 1:100, or from about 1:10 to about 1:50. For example, thesample can be diluted such that only a single fragment of nucleic acidis present per 500 nanoliters of diluted sample, or per 200 nanolitersof diluted sample. In some embodiments, the concentration of targetfragments can be based on the size of theimmiscible-fluid-discrete-volumes generated that carry the targetfragments, such that an average of about 1 target fragment is presentper 1.4 immiscible-fluid-discrete-volumes generated. According tovarious embodiments, the sample can be diluted such that at least 50%immiscible-fluid-discrete-volumes produced from a sample in the processdescribed below can each comprise a single target nucleic acid sequence.In various other embodiments, less than about 50% of theimmiscible-fluid-discrete-volumes produced can each comprise a singletarget nucleic acid sequence. In other embodiments, at least 1% or more,5% or more, 10% or more, or 20% or more can comprise a single targetnucleic acid sequence, for example, from about 10% to about 50% or fromabout 20% to about 40%.

After optional preprocessing, the sample fluid is introduced to system10 to fort one or more discrete volumes of the sample fluid in a spacingfluid with which it is immiscible. According to various embodiments, themethod can comprise forming immiscible-fluid-discrete-volumes ofdiscrete amounts of sample fluid and/or reagents inside conduit system50. A plurality of immiscible-fluid-discrete-volumes can be associatedtogether as a set of immiscible-fluid-discrete-volumes. Each set ofimmiscible-fluid-discrete-volumes can compriseimmiscible-fluid-discrete-volumes separated from one another by aspacing fluid, for example, an oil. Eachimmiscible-fluid-discrete-volume of a set can be equally spaced from oneor more adjacent immiscible-fluid-discrete-volumes of the set. Multiplesets of immiscible-fluid-discrete-volumes can be present at the sametime in main conduit 50. Each set of immiscible-fluid-discrete-volumescan be separated from one or more other sets ofimmiscible-fluid-discrete-volumes by spacing fluid. In some embodiments,two or more sets of immiscible-fluid-discrete-volumes are spaced fromone another a distance that is greater than the average distance betweenadjacent immiscible-fluid-discrete-volumes with the same set.

In the embodiment depicted in FIGS. 1A and 1B,immiscible-fluid-discrete-volumes that have been aspirated intoimmiscible-fluid-discrete-volume-forming conduit 12 can be moved intoholding conduit 56 by suction produced by vacuum pump 40.

According to various embodiments, a sample to be subjected to de novosequencing can comprise a single copy of the genomic DNA of an organism.The sample DNA can be sheared, and universal tails can be ligated to thesample. Nucleic acid amplification reactants can be added to the samplebefore the sample is drawn into system 10 or after the sample has beendrawn into system 10. The nucleic acid amplification reactants cancomprise universal primers, for example, primers that are specific tothe universal tail sections ligated to the sample nucleic acidfragments. The sample can be diluted such that when the sample is madeinto immiscible-fluid-discrete-volumes by system 10, eachimmiscible-fluid-discrete-volume does not contain more than one nucleicacid fragment. For example, 2, 3, 4, or 5 out of tenimmiscible-fluid-discrete-volumes can contain nucleic acid fragments.

According to some embodiments, the method can comprise moving a set ofimmiscible-fluid-discrete-volumes, from T-junction 52, to cross-junction70, by way of conduit system 50. If a set ofimmiscible-fluid-discrete-volumes does not contain nucleic acidamplification reactants, the reactants can be added to eachimmiscible-fluid-discrete-volume of the set ofimmiscible-fluid-discrete-volumes at cross-junction 70. Reactantaddition to each immiscible-fluid-discrete-volume can be metered byrotary valves 71 and 73. Detector D-3 can detect the arrival of thebeginning and/or the end of a set of sampleimmiscible-fluid-discrete-volumes at cross-junction 70. Detector D-21can detect the arrival of the beginning and/or the end ofimmiscible-fluid-discrete-volumes at cross-junction 70. Valve V-7 cancontrol the movement of a set of immiscible-fluid-discrete-volumes outof cross-junction 70.

According to some embodiments, the method can comprise moving a set ofimmiscible-fluid-discrete-volumes from cross-junction 70, through mainconduit system 50, to thermal spiral 74. Detector D-8 can be used todetect the arrival of a set of immiscible-fluid-discrete-volumes atthermal spiral 74. Detector D-8 can be used to detect the end of a setof immiscible-fluid-discrete-volumes, and thereby detect that a set ofimmiscible-fluid-discrete-volumes is disposed in thermal spiral 74. Aset of immiscible-fluid-discrete-volumes can be thermally cycled, forone or more cycles, for example, for from about 5 to about 50temperature cycles or from about 20 to about 30 temperature cycles.

According to various embodiments, the method can comprise introducingpolymerase chain reaction inactivating reagents into main conduit 50after amplifying the at least one target nucleic acid sequence andbefore subjecting the nucleic acid sequence to a sequencing reaction.The reagents can be used to inactivate or remove or eliminate excessprimers an/or dNTP's. The inactivating reagents can be introduced at anjunction in the conduit, for example, after animmiscible-fluid-discrete-volume to be inactivated is aligned with thejunction. The junction can comprise, for example, a T-junction.

According to some embodiments the method can comprise moving a set ofimmiscible-fluid-discrete-volumes from thermal spiral 74, throughcross-junction 76. As the set of immiscible-fluid-discrete-volumes movesthrough cross-junction 76, the method can comprise adding exonucleaseand shrimp alkaline phosphatase to each immiscible-fluid-discrete-volumeof the set of immiscible-fluid-discrete-volumes. For example, theexonuclease and shrimp alkaline phosphatase can be metered out indiscrete volumes which merge respectively with theimmiscible-fluid-discrete-volumes of a set ofimmiscible-fluid-discrete-volumes at an junction in rotary valve 77. Forexample, exonuclease and shrimp alkaline phosphatase can be added toeach immiscible-fluid-discrete-volume of the set ofimmiscible-fluid-discrete-volumes in cross-junction 76.

In the exemplary system shown, detector D-6 can detect the arrival ofthe beginning and/or the end of a set of sample discrete volumes atcross-junction 76. Detector D-18 can detect the arrival of the beginningand/or the end of one or more immiscible-fluid-discrete-volumes ofexonuclease and shrimp alkaline phosphatase at cross-junction 76. ValveV-8 can control the movement of a set ofimmiscible-fluid-discrete-volumes out of cross-junction 76.

In the exemplary embodiment shown, a set ofimmiscible-fluid-discrete-volumes containing exonuclease and shrimpalkaline phosphatase can be moved into thermal spiral 80, via mainconduit system 50. Detector D-9 can detect the arrival of the beginningand/or the end of a set of immiscible-fluid-discrete-volumes at thermalspiral 80. The set of immiscible-fluid-discrete-volumes can be incubatedat from about 25° C. to about 35° C. for a time period of from about oneminute, to about 60 minutes or from about two minutes to about 10minutes. The incubation step can function to facilitate the activitiesof the exonuclease and shrimp alkaline phosphatase. A set ofimmiscible-fluid-discrete-volumes can be further incubated at atemperature of from about 75° C. to about 85° C., for a time period offrom about 10 seconds to about 10 minutes, or from about one minute toabout five minutes. The incubation at from about 75° C. to about 85° C.can function to heat-kill any enzymes that might still be present in theset of immiscible-fluid-discrete-volumes. After such incubation,processed immiscible-fluid-discrete-volumes can be maintained in aconduit section held at a lower temperature, for example, at about 25°C., in a stretch of conduit if it is desired to delay delivery of theimmiscible-fluid-discrete-volumes to the cycle sequencing section of thesystem. In such circumstances a delay can be built into the system sothat a first set of immiscible-fluid-discrete-volumes can be completelycycle sequenced while a second batch awaits movement into the cyclesequencing section of the system.

According to some embodiments, the method can comprise moving a set ofimmiscible-fluid-discrete-volumes to T-junction 84. Valve V-9 cancontrol the movement of a set of immiscible-fluid-discrete-volumes fromthermal spiral 80, to T-junction 84. Detector D-10 can detect thearrival of the beginning and/or the end of a set ofimmiscible-fluid-discrete-volumes at T-junction 84. The method cancomprise dividing one or more immiscible-fluid, discrete volumes of aset of immiscible-fluid discrete volumes into two or more smallerimmiscible-fluid-discrete volumes to form two newly formed sets of equalnumber of immiscible-fluid discrete volumes, but containingimmiscible-fluid discrete volumes of smaller volume. The method cancomprise moving one newly created set of immiscible-fluid, discretevolumes along main conduit system 50, to cross-intersection 86. Forwardprimers and chain terminating dyes can be moved from reservoirs 91 and93, to rotary valve 77. The forward primers and chain terminating dyescan be metered out by rotary valve 77. The forward primers and chainterminating dyes can be moved to cross-intersection 86 and be added toeach immiscible-fluid-discrete-volume of the newly-created set ofimmiscible-fluid, discrete volumes, thereby creating a forward set ofimmiscible-fluid, discrete volumes. According to various embodiments,the method can comprise moving the second newly created set ofimmiscible-fluid, discrete volumes along main conduit system 50, tocross-intersection 88. Reverse primers and chain terminating dyes can bemoved from reservoirs 95 and 97, to rotary valve 79. The reverse primersand chain terminating dyes can be metered out by rotary valve 79. Thereverse primers and chain terminating dyes reagent can be moved tocross-intersection 86 and be joined with eachimmiscible-fluid-discrete-volume of the second newly-created set ofimmiscible-fluid, discrete volumes, thereby creating a reverse set ofimmiscible-fluid, discrete volumes.

In some embodiments, the method can comprise moving the forward set ofimmiscible-fluid-discrete-volumes from cross-junction 86, along mainconduit system 50, to thermal spiral 90. The forward set ofimmiscible-fluid-discrete-volumes can be thermally cycled for from about5 to about 50, temperature cycles, for example, from about 20 to about40 thermal cycles.

In some embodiments, the method can comprise moving the reverse set ofimmiscible-fluid-discrete-volumes from cross-junction 88, along mainconduit system 50, to thermal spiral 92. The reverse set ofimmiscible-fluid-discrete-volumes can be thermally cycled for from about5 to about 50 thermal cycles, for example, from about 20 to about 40cycles, temperature cycles.

According to various embodiments, the method can comprise moving theforward and the reverse sets of immiscible-fluid-discrete-volumes fromtheir respective thermal spiral to output conduit 54. Movement can becaused by syringe pumps 82A and 82B that can be controlledindependently, or together, by a motor 88A operatively connectedthereto. Syringe pumps 82A and 82B can push and pull fluids throughrespective T-junctions 84A and 84B. This arrangement is useful assyringe pumps 82A and 82B can initially pullimmiscible-fluid-discrete-volumes into place in the respective thermalspirals 90 and 92, in conjunction with the positive pressure from thepumps on the upstream side of tee 84. Valves V-10 and V-11 can beswitched so that immiscible-fluid-discrete-volumes can be pushed out ofsystem 10. In some embodiments, the pushing can be done with one ofpumps 82A and 82B at a time; therefore, there is no need to merge twoseparate sets of immiscible-fluid-discrete-volumes back together into asingle set, but rather the separate sets can be individually dispensed.Output conduit 54 can deposit both sets ofimmiscible-fluid-discrete-volumes on, for example, a multi-well plate.

According to some embodiments, a dye can be added to one or moreimmiscible-fluid-discrete-volumes of a set ofimmiscible-fluid-discrete-volumes. The dye can comprise a double-strand(ds), nucleic acid intercalating dye, for example, SYBR green, SYBRgold, EVA green, LC green, or the like. The dye can be added to anaqueous immiscible-fluid-discrete-volume-forming fluid, such as anaqueous sample, before it is added to system 10. The dye can be added toa set of immiscible-fluid-discrete-volumes at any cross-junction ofsystem 10. The dye can be used to discriminate betweenimmiscible-fluid-discrete-volumes that contain ds nucleic acids andimmiscible-fluid-discrete-volumes that do not contain ds nucleic acids.The immiscible-fluid-discrete-volumes that do not contain ds nucleicacids can be removed from output conduit 54 before theimmiscible-fluid-discrete-volumes are deposited on a multi-well plate47. The immiscible-fluid-discrete-volumes that do not contain ds nucleicacids can be moved through second waste conduit system 48, to wastereservoir 85. In some embodiments, a dye can be detected by detector 98to determine whether a discrete volume should be sent to second wastereservoir 85 or be collected. Pump 87 can apply a negative pressure towaste conduit system 48, which can cause the movement ofimmiscible-fluid-discrete-volumes into waste reservoir 85.

Immiscible-fluid-discrete-volumes deposited on multi-well plate 47 canbe subjected to a sequencing reaction to form a detectable product, andthe method of the present teachings can comprise detecting thedetectable product. In various embodiments, the detectable product canbe detected using, for example, a flow cell or a capillaryelectrophoretic sequencer. In various other embodiments, anoff-capillary detector can be used as deemed appropriate.

Shown below is Table 1, which shows a state diagram of various settingsthat can be implemented for the various valves and detectors of thesystem shown in FIGS. 1A and 1B, to achieve various different functions,for example, an embodiment of the de novo sequencing method describedabove.

TABLE 1 V-1 V-2 V-3 V-4 V-5 V-6 V-7 V-8 V-9 V-10 V-11 V-12 V-13 V-14V-15 V-16 Prime SMA Sample 0 1 0 1 0 0 0 0 1 0 1 0 0 0 0 1 0 1 0 0 0Deliver initial 0 1 0 1 0 0 0 portion of SMAF/MM mixture to ZT-1 0 0 1 01 0 0 0 Deliver initial 0 0 0 0 0 0 0 0 1 1 0 1 portion of oil to ZT-1Form initial SMAF 0 0 1 0 1 0 1 0 0 1 1 0 1 Zebra Deliver intermediate 01 0 1 0 0 portion(s) of SMAF.MM mixture toZT-1 0 0 1 0 1 0 1 0 0 1 1 0 1Deliver final 0 1 0 1 0 0 portion(s) of SMAF.MM mixture toZT-1 0 0 1 0 10 1 0 0 1 1 0 1 Amplify DNA 0 0 Prime ES reagent 0 0 1 1 path 0 0 1 1Add ES reagents and 0 0 1 1 1 1 1 0 1 1 0 1 load clean up thermal cycler0 0 1 1 1 1 1 0 1 1 0 1 Clean up after PCR 0 0 Prime PF + BD paths 0 0 00 0 0 Add FP + BD and 0 0 1 1 1 1 1 0 1 1 0 1 RP + BD & load 0 0 1 1 1 11 0 1 1 0 1 cycle sequencing sticky bun Cycle sequence 0 0 0 Dispensesample- 0 0 1 1 1 1 0 0 1 1 0 1 laden FP slugs to 0 0 1 1 1 1 0 0 1 1 01 tray, dispose of other fluids Rotary Rotary V-17 V-18 V-19 V-20 V-21V-22 V-23 V-24 V-25 V-26 Valve-ES Valve-FP&BD Prime SMA Sample 1 0 1 0 01 0 0 1 Deliver initial 1 0 1 portion of SMAF/MM mixture to ZT-1 1 0 1Deliver initial 0 0 0 0 1 portion of oil to ZT-1 Form initial SMAF 0 1 10 0 0 1 Zebra Deliver intermediate 1 1 1 portion(s) of SMAF.MM mixturetoZT-1 0 1 0 0 0 0 1 Deliver final 1 1 1 portion(s) of SMAF.MM mixturetoZT-1 0 0 0 0 1 Amplify DNA 0 0 Prime ES reagent 1 Oil path out 1 ESout Add ES reagents and 0 0 0 0 0 0 out 0 load clean up thermal cycler 00 0 0 0 0 0 0 Clean up after PCR Prime PF + BD paths 1 1 Oil out FP BD 11 Oil out Add FP + BD and 0 0 0 0 0 0 0 out RP + BD & load 0 0 0 0 0 0 00 cycle sequencing sticky bun Cycle sequence 0 0 0 Dispense sample- 0 00 0 0 0 1 0 0 laden FP slugs to 0 0 0 0 0 0 0 0 0 tray, dispose of otherfluids Rotary Valve- Rotary SP- SP- SP- MM_SMF Valve-MM_VI VICI-1 VICI-2MM SPES FP&BD RP&BD Footnote Prime SMA Sample 0 1 1 Oil 0 1 2 MM 0 1 3Deliver initial MM 0 1 4 portion of SMAF/MM mixture to ZT-1 MM 0 1 5Deliver initial Off 0 1 6 portion of oil to ZT-1 Form initial SMAF 7Zebra Deliver intermediate MM 0 1 8 portion(s) of SMAF.MM mixture toZT-11 1 9 Deliver final MM 0 1 10 portion(s) of SMAF.MM mixture toZT-1 1 111 Amplify DNA Prime ES reagent 12 path 13 Add ES reagents and 0 0 1 0out 0 0 14 load clean up thermal cycler 0 0 1 0 0 0 0 15 Clean up afterPCR Prime PF + BD paths 16 Oil In In 17 out out out In In 18 RF In In 19BD In In 20 Oil In In 21 out out out Add FP + BD and out 1 0 0 0 1 1 22RP + BD & load 0 1 0 0 0 0 0 cycle sequencing sticky bun Cycle sequence0 Dispense sample- 0 1 23, laden FP slugs to 0 1 24 tray, dispose ofother fluids Footnotes: ¹Pull SMAF into T-intersection (67); ²Pull oilthrough T-intersection (67); ³Pull MM through T-intersection (67); ⁴PullSMAF + MM through D-17; ⁵Push SMAF + MM towards T-intersection (66)until D-5 detects AF; ⁶Pull, Push oil towards T-intersection (66) untilD-4 detects oil; ⁷Push oil + SMAF + MM through thermal cycler until D-6detects zebras or, more likely, D-2 sees only oil; ⁸Pull SMAF + MMthrough D-17; ⁹Push oil + SMAF + MM through thermal cycler until D-6detects zebras or, more likely, D-2 sees only oil; ¹⁰Pull SMAF + MMtowards D-17. After total volume of SMAF has entered T-intersection(67), close V-18. After total volume of MM has left Rotarty Valve (71),switch Rotary Valve (71) to “oil” position. Continue pulling SMAF + MMtowards D-17 until D-2 sees a; ¹¹Push oil + SMAF + MM through thermalcycler until D-6 detects zebras or, more likely, D-5 sees only oil;¹²Push oil until D-16 detects oil; ¹³Push ES until D-18 detects ES, thenpush further distance calculated to advance ES to Zebra path.; ¹⁴Pushuntil D-6 detects end of batch, then push further distance calculated toadvance batch just past ES adder; ¹⁵Push until D-9 detects end of batch,then push farther distance calculate to advance batch completely intocleanup thermal cycler; ¹⁶Push SP (78) until D-19 sees oil. Push SP (82)until D-20 sees oil.; ¹⁷Pull portion of FP into SP (78). Pull portion ofRP into SP (82); ¹⁸Pull portion of BD into SP (78). Pull portion of BDinto SP (82); ¹⁹Pull alternating sub-portions of primers and big dyesuntil complete portion has been loaded; ²⁰Pull small amount of oil soall aqueous fluids advance into syringe; ²¹Push SP (78) until D-19 seesFP + BD. Push SP (82) until D-20 sees RP + BD. Push farther distancecalculated to advance FP + BD and RP + BD to Zebra path; ²²Push withpumps until D-11 and D-7 see oil, then push further distance calculatedto advance batch just past RP + BD and FP + BD adders; ²³Push with pumpsfurther distance calculated to advance batch into cycle sequencingthermal cycler; ²⁴Push until FSD-1 detects sample-laden FP slug, thenpush further distance calculated to move downstream boundary ofsample-laden slug just inside dispense tip; ²⁵Push distance calculatedto bead sample-laden slug on dispense tip. Touch bead to bottom ofsample well.

According to various embodiments, the present teachings can encompass aresequencing method using system 10. In general, the resequencing methodis similar to the de-novo method described herein with modifications asdiscussed herein.

In some embodiments, the pre-processing of a sample for resequencingcomprises shearing a robust sample of nucleic acid having a plurality ofcopies of one or more nucleic acids of interest, herein also referred toas target sequences. The nucleic acids in the sample can be sheared. Themethod can comprise adding a plurality of gene specific zip code primersto the sample before introduction to system 10, or the gene specific zipcode primers can be added, at for example, at cross-junction 10, to aset of immiscible-fluid-discrete-volumes generated from the sample.Immiscible-fluid-discrete-volumes made from the sample can contain asingle copy of a nucleic acid fragment or can contain a plurality ofcopies of one or more different nucleic acid fragments. Eachimmiscible-fluid-discrete-volume can contain, for example, from about 50to about 150 different gene-specific zip code primers. The gene-specificzip code primers can be present at a relatively low concentration.Exemplary low concentrations can comprise from about 0.1 nanomolarprimers per nanoliter (primers/nl) to about 1 micromolar primers/nl, orfrom about 10 nanomolar primers per nanoliter (primers/nl) to about 50nanomolar primers/nl.

According to some embodiments, the method can comprise addingsequence-specific zip code primers, specific to a single zip codesequence, to each immiscible-fluid-discrete-volume of a set ofimmiscible-fluid-discrete-volumes. The sequence-specific zip codeprimers added to each immiscible-fluid-discrete-volume can be differentfor one immiscible-fluid-discrete-volume than for at least one otherimmiscible-fluid-discrete-volume, and can be complementary to the zipcode sequences of a specific set of gene-specific zip code primers. Thesequence-specific zip code primers can be present in a highconcentration relative to the concentration of the gene-specific zipcode primers. For example, the concentration of the sequence specificzip code primers can be in excess, and the concentration of the genespecific zip code primers can be limiting. The concentration of thesequence specific zip code primers can be present, relative to theconcentration of the gene-specific zip code primers, at, for example, aratio of from about 10 nanomolar to about 1 micromolar, or from about100 nanomolar to about 500 nanomolar.

In some embodiments, the method can comprise moving a set ofimmiscible-fluid-discrete-volumes comprising the concentrations ofprimers discussed above, to thermal spiral 74. The set ofimmiscible-fluid-discrete-volumes can be thermally cycled and thereafterprocessed in any of the many manners disclosed herein for the de novosequencing method. Various sequencing and re-sequencing methods that canbe carried out according to various embodiments can include, forexample, those depicted in FIGS. 2C-2K of co-pending U.S. patentapplication Ser. No. ______, filed Aug. 22, 2006, entitled “Apparatus,System, and Method Using Immiscible-Fluid-Discrete-Volumes,” to Lee etal. (attorney docket number 5010-362), which is incorporated herein inits entirety by reference.

Shown below are Tables 2A and 2B which are the first and second halvesof another state diagram of various settings that can be implemented forthe various valves and detectors of the system ho in FIGS. 1A and 1B, toachieve various different functions. The various functions can includecarrying out various different immiscible-fluid-discrete-volumeprocessing, for example, carrying out the standard resequencingreactions depicted in FIGS. 2C-2D of U.S. patent application Ser. No.______, filed Aug. 22, 2006, entitled “Apparatus, System, and MethodUsing Immiscible-Fluid-Discrete-Volumes,” to Lee et al. (attorney docketnumber 5010-362).

TABLE 2A V-1 V-2 V-3 V-4 V-5 V-6 V-7 V-8 V-9 V-10 V-11 V-12 V-13 V-14V-15 V-16 V-17 V-18 Prime Primary 0 0 0 0 0 1 0 1 VI Input Path Form VIZebra 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 0 0 0 0 0 1 0 1 00 0 0 0 1 0 1 Push Zebra 0 0 0 0 1 1 0 1 0 Into Storage Repeat “Form VIZebra” and “Push Zebra Into Storage” until D-4 sees zebras or until thetotal required number of slugs is reached. Prime Secondary 1 1 0 1 0 0 00 0 VI Input Path Form secondary 1 1 0 1 0 0 0 0 0 VI fluid 1 1 0 1 0 00 0 0 macro slugs 1 1 0 1 0 0 0 0 0 Push Macro- 0 1 0 0 0 Zebra IntoStorage Repeat “Form secondary VI fluid macro slugs” and “PushMacro-Zebra Into Storage” until D-4 sees zebras or until the totalrequired number of slugs is reached. Add Secondary 0 1 0 0 1 0 0 0 1 1 01 0 VI fluid to Zebra slugs Prime MM_VI Add MM to VI 0 1 0 0 1 1 0 0 1 10 1 0 Zebra slugs Amplify DNA 0 0 Rotary Rotary Rotary Rotary RotaryValve Valve Valve Valve Valve V-19 V-20 V-21 V-22 V-23 V-24 V-25 V-26(75) (77) (71) (73) (79) Prime Primary VI Input Path Form VI Zebra PushZebra 1 1 Into Storage Repeat “Form VI Zebra” and “Push Zebra IntoStorage” until D-4 sees zebras or until the total required number ofslugs is reached. Prime Secondary 0 1 VI Input Path Form secondary 0 1VI fluid 0 1 macro slugs 0 1 Push Macro- 1 0 Zebra Into Storage Repeat“Form secondary VI fluid macro slugs” and “Push Macro-Zebra IntoStorage” until D-4 sees zebras or until the total required number ofslugs is reached. Add Secondary 1 0 0 1 0 0 VI fluid to Zebra slugsPrime MM_VI 0 MM Add MM to VI 1 0 0 0 1 Out Zebra slugs Amplify DNA 0 0Pump Pump SP SP SP SP (40) (39) (58) (66) (78) (82) Prime Primary 1 Pulloil from reservoir until it reaches D-15, then pump distance calculatedto VI Input Path advance oil at D-17 just past V-17. Form VI Zebra 1Pull 78 nl primary VI fluid into tube through tip. Wash tip. 1 Pull 800nl oil into tube through tip. Wash tip. 1 Pull 78 nl primary VI fluidfrom next well into tube through tip. Wash tip. 1 Pull 800 nl oil intotube through tip. Wash tip. 1 Continue aspiration steps until zebras(sequence of immiscible fluid volumes) are detected by D-15. Push Zebra1 Push oil until D-16 no longer sees slugs (individual fluid volumes).Into Storage Repeat “Form VI Zebra” and “Push Zebra Into Storage” untilD-4 sees zebras or until the total required number of slugs is reached.Prime Secondary 1 Pull oil from reservoir until it reaches D-17, thenpump distance calculated to VI Input Path advance oil at D-17 just pastV-17. Form secondary 1 Pull m(78 nl) of secondary VI fluid i into tube,where m is the VI fluid number of primary VI fluids that are to be mixedwith the ith secondary fluid. macro slugs 1 Pull 800 nl oil into tubethrough tip. Wash tip. 1 Continue aspiration steps until zebras aredetected by D-17. Push Macro- Pump oil to push macro-zebra until D-2 nolong sees macro-slugs. Zebra Into Storage Repeat “Form secondary VIfluid macro slugs” and “Push Macro-Zebra Into Storage” until D-4 seeszebras or until the total required number of slugs is reached. AddSecondary 1 1 0 Push micro and macro zebras until D-3 sees slugs VIfluid to Zebra slugs Prime MM_VI 1 Load Syringe Pump (58) Add MM to VI 11 1 Runs pumps until D-6 sees slugs Zebra slugs Amplify DNA

TABLE 2B V-1 V-2 V-3 V-4 V-5 V-6 V-7 V-8 V-9 V-10 V-11 V-12 V-13 V-14V-15 V-16 V-17 V-18 Prime ES Reagent path 0 0 1 1 0 0 1 1 Add ESReagents 0 0 1 1 1 1 1 0 1 1 0 1 0 & load cleanup thermal cycler 0 0 1 11 1 1 0 1 1 0 1 0 Clean up after PCR 0 0 Prime FP + BD and RP + BD paths0 0 0 0 0 0 Add FP + BD and 0 0 1 1 1 1 1 0 1 1 0 1 0 RP + BD & loadcycle sequencing 0 0 1 1 1 1 1 0 1 1 0 1 0 thermal cycler Cycle sequence0 0 0 Dispense sample- 0 0 1 1 1 1 0 0 1 1 0 1 0 laden FP slugs to tray,dispose of 0 0 1 1 1 1 0 0 1 1 0 1 0 other fluids Rotary Rotary RotaryRotary Rotary Valve Valve Valve Valve Valve Pump Pump SP V-19 V-20 V-21V-22 V-23 V-24 V-25 V-26 (75) (77) (71) (73) (79) (40) (39) (58) PrimeES Oil Reagent path 1 Out ES 1 Out Add ES Reagents 0 0 0 0 0 Out 0 0 0 10 0 & load cleanup thermal cycler 0 0 0 0 0 0 0 0 0 1 0 0 Clean up afterPCR Prime FP + BD Oil Oil and RP + BD paths 1 1 Out Out FP RP BD BD OilOil 1 1 Out Out Add FP + BD and 0 0 0 0 0 0 Out 0 Out 1 0 0 RP + BD &load cycle sequencing 0 0 0 0 0 0 0 0 0 1 0 0 thermal cycler Cyclesequence 0 0 0 0 Dispense sample- 0 0 0 0 0 1 0 0 0 0 1 laden FP slugsto tray, dispose of 0 0 0 0 0 0 0 0 0 0 1 other fluids SP SP SP (66)(78) (82) Prime ES In Reagent path Out Push oil until D-18 detects oil.In Out Push ES until D-18 detects ES, then push further distancecalculated to advance ES to zebra path. Add ES Reagents Out 0 0 Pushuntil D-6 detects end of batch, then push further distance calculated toadvance batch just past ES & load cleanup adder. thermal cycler 0 0 0Push until D-9 detects end of batch, then push further distancecalculate to advance batch completely into cleanup thermal cycler. Cleanup after PCR Prime FP + BD In In and RP + BD paths Out Out Push SP-FP&BDuntil D-19 sees oil. Push SP (82) until D-20 sees oil. In In Pullportion of FP into SP (78). Pull portion of RP into SP-RP&BD. In In Pullportion of BD into SP (78). Pull portion of BD into SP (82). Pullalternating sub-portions of primers and big dyes until complete portionhas been loaded. In In Pull small amount of oil so all aqueous fluidsadvance into syringe. Out Out Push SP (78) until D-19 sees FP + BD. PushSP (82) until D-20 sees RP + BD. Push farther distance calculated toadvance FP + BD and RP + BD to zebra path. Add FP + BD and 0 1 1 Pushwith pumps until D-11 and D-7 see oil, then push further distancecalculated to advance batch just past RP + BD & load RP + BD and FP + BDadders. cycle sequencing 0 0 0 Push with pumps further distancecalculated to advance batch into cycle sequecning thermal cycler.thermal cycler Cycle sequence Dispense sample- Push until fluorescentdetector (98) detects sample-laden FP slug, then push further distancecalculated to laden FP slugs to move downstream boundary of sample-ladenslug just inside dispense tip. tray, dispose of Push distance calculatedto bead sample-laden slug on dispense tip. Touch bead to bottom ofsample well. other fluids

FIG. 1C is yet another system for processing immiscible-fluid-discretevolumes downstream of the apparatuses, methods, and systems disclosedherein.

A simplified system 5600 is illustrated in FIG. 1C As illustrated, box5602 represents a structure that delivers to tube 5604 of system 5600discrete volumes 5606 of aqueous liquid in a non-aqueous liquid 5608with which they are immiscible. Examples of such structures and methodsof generating discrete volumes 5606 in contact with spacing fluid 5608are described herein. In some embodiments, such a structure could be atube of preformed discrete volumes 5606 of aqueous fluid. In someembodiments, such a structure could be a chip or other substrate with achannel therein containing the discrete volumes 5606 of aqueous fluid.As illustrated, tube 5604 extends throughout system 5600. After enteringtube 5604, desired information about aqueous volumes 5606 are determinedand optionally manipulated by structures in triangle 5610. For example,the length and speed of a slug and the distance between two adjacentslugs can be desired information. In that example, a slug detectionsystem can provide that information. If the distance between adjacentslugs does not meet preferred values, then additional spacing fluid canbe added between the trailing point of the first slug and the leadingpoint of the second slug, or one of the slugs could be held in anelectric field, for example, to allow more of the existing spacing fluidto flow past it in tube 5603. If the length, and therefore the volume,of an aqueous discrete volume does not meet preferred values, additionalnon-reactive, miscible liquid can be added by an apparatus at that areaof tube 5604. Triangle 5610 represents these and other structures ofdiscrete volume characteristic detection and manipulation. Examples ofthese structures and/or component parts of thereof are described herein.

System 5600, as illustrated in FIG. 1C, next incorporates a processingsection 5612 of tube 5604 (not illustrated, but in the box), which caninclude, for example, vibration, heating, cooling, and electromagneticradiation exposure. In some embodiments, processing section 5612 caninclude thermal cycling between one or more pre-determined temperaturesfor pre-determined durations as needed, for example, to perform PCR, orother amplification methods. In some embodiments, aqueous discretevolumes may continue to flow at a constant rate through processingsection 5612 while undergoing a desired process, or alternatively, theymay dwell in a particular location in processing section 5612. System5600, as illustrated in FIG. 1C, includes another aqueous discretevolume characteristic determination and optional manipulation station5614. Aqueous discrete volumes 5606 then flow through a junction J-1. Insome embodiments, junction J-1 can be a T. As illustrated, fluidaddition station 5620 includes pump P-1 and valve V-1 in conjunctionwith a supply of different fluid (not shown) and can add that fluid totube 5604. In some embodiments, a gas phase can be introduced betweenaqueous discrete volumes 5606. In some embodiments, an aqueous liquidcan be added to aqueous discrete volumes 5606 in junction J-1. In someembodiments, the different aqueous fluid can be added a discrete volumebetween aqueous discrete volumes 5606. An aqueous discrete volumecharacteristic determination and optional manipulation station 5615,like 5614 and 5610 described above, follows liquid addition station5620. In some embodiments, station 5615 evaluates the volume of liquidadded to aqueous discrete volume 5606.

Next in line, as illustrated in FIG. 1C, is junction J-2. Junction J-2and junction J-4, further down the line, fluidically connect backpressure unit 5616 to pressurize tube 5604 to a desired pressure.Between junctions J-2 and J-4, system 5600 includes a second processingsection 5612, a junction J-3, at which point, fluid adding station 5622can add a volume of liquid to pre-existing aqueous discrete volumes5606, and an aqueous discrete volume characteristic determination andoptional manipulation station 5617 can evaluate the volume of liquidadded to aqueous discrete volume 5606.

As illustrated in FIG. 1C, system 5600 includes a final processingsection 5612, and processed aqueous discrete volumes are delivered fromtube 5604 to output station 5618. Examples of structures used in outputstation 5618 can include those described herein.

Reference will now be made to various embodiments of devices, apparatus,systems, and methods for depositing immiscible-fluid-discrete-volumes ofa first fluid separated from one another by an immiscible spacing fluid,examples of which are illustrated in the accompanying drawings. Variousembodiments of these can be used in the system described above withreference to FIGS. 1A and 1B. Wherever possible, the same referencenumbers are used in the drawings and the description to refer to thesame or like parts.

As shown in FIG. 2, according to embodiments of the present teachings,an immersion plate 102 can be provided on which to deposit of aqueousdrops, for instance sample drops, in a pattern on a top surface ofimmersion plate 102. According to various embodiments, the depositedaqueous drops can be formed in a pattern aligned with the capillary tipsof a capillary electrophoresis array or other processing device.According to various embodiments as shown in FIG. 2, immersion plate 102can be filled with and contain a fluid 116, such as an oil, covering abottom of a shallow, open cavity or recess of immersion plate 102.According to various embodiments, the surface of the open cavity orrecess of immersion plate 102 can have areas that possess hydrophilicfeatures, the hydrophilic features being surrounded by, for example,hydrophobic features or areas. According to various embodiments, theimmersion plate 102 can receive a discharge tip 108 or other outletnozzle of an immiscible-fluid-discrete-volume conduit 104 in the opencavity or recess of immersion plate 102. According to variousembodiments in one regard, discharge tip 108 ofimmiscible-fluid-discrete-volume conduit 104 can be positioned underrobotic control over, for example, hydrophilic areas of the bottomsurface of immersion plate 102.

According to various embodiments as shown in FIG. 2,immiscible-fluid-discrete-volume conduit 104 can contain a set ofaqueous discrete volumes 106, for example such as aqueous samplediscrete volumes, that are separated by spacing fluid 110. According tovarious embodiments, spacing fluid 110 can be an oil, such as variousoil formulations immiscible with aqueous discrete volumes 106, asdescribed herein. According to various embodiments, pressure or vacuumcan for example be applied to immiscible-fluid-discrete-volume conduit104 to cause the discharge and deposition of aqueous discrete volumes106 on a top surface of immersion plate 102. According to variousembodiments, aqueous discrete volumes 106 can be injected onto desiredareas of immersion plate 102 using other types of force, for exampleelectrokinetic injection. According to various embodiments, spacingfluid 110 and fluid 116 can be the same fluid, such as the same oil.

As shown in FIG. 3, showing an enlarged view of a deposition arealabeled A in FIG. 2, according to various embodiments, immersion plate102 can have formed, on a surface of a shallow cavity or recess therein,a set of hydrophilic features 112. According to various embodiments,hydrophilic features 112 can be gold contact areas, such aselectroplated dots or other feature shapes. It will be appreciated thatwhile FIG. 3 illustrates three hydrophilic features as slightly raisedcontact areas and one as a depression with a rim around it, on a bottomsurface of a shallow inner cavity or recess of immersion plate 102, invarious embodiments hydrophilic features 112 can be formed in otherconfigurations, such as lining the surface of a well or recess, formedflush in immersion plate 102, recessed in a surface of immersion plate102 without a retaining rim, or the like. Other configurations ofhydrophilic features 112 are also possible.

According to various embodiments, as shown in FIG. 3,immiscible-fluid-discrete-volume conduit 104 can deposit a set ofdeposited drops 114 deposited in contact with respective ones ofhydrophilic features 112. More specifically, in embodiments as shown,immiscible-fluid-discrete-volume conduit 104 can be moved, for exampleunder robotic control, sequentially over the locations of hydrophilicfeatures 112. When discharge tip 108 is positioned over a next one ofhydrophilic features 112, pressure or other force can be applied toimmiscible-fluid-discrete-volume conduit 104, for example, by syringepump, to expel a next one of aqueous volumes 106 to contact theunderlying one of hydrophilic features 112, and thereby form a next oneof deposited drops 114. According to various embodiments as shown,deposited drops 114 can be immersed below immersion fluid 116, such asan oil that is less dense than water. In some embodiments where spacingfluid 110 is heavier than water, spacing fluid 110 can be vacuumed awayfrom tip 108 with a waste removal system such as that described withreference to FIGS. 4B, 5A, 12, 30 and 31. Alternatively, spacing fluid110 can be collected in receptacles, for example, troughs 115 disposedbetween hydrophilic features 112.

According to various embodiments in one regard, aqueous volumes 106 cancontain sample material that has been subjected to polymerase chainreaction (PCR) with one sulfhydryl-labeled primer, forming ampliconsthat are deposited as deposited drops 114 on hydrophilic features 112 ofimmersion plate 102. According to various embodiments, the shallowcavity or recess of immersion plate 102 can be immersed under fluid 116,deposited drops 114 do not evaporate, allowing, for example, agold-thiol bond to form. According to various embodiments, the otherstrand can be stripped off, and sequencing extension and washing andinjection can be performed, as for example described elsewhere herein.In some embodiments, an injection fluid can be added to the hydrophilicfeatures, for example, under robotic control, to create similar-sizedentrapped aqueous portions on the plate for injection purposes.According to various embodiments, immersion plate 102 can be re-immersedwith fresh fluid 116, for example, injection fluid as described herein,while retaining bound analytes on hydrophilic features 112. According tovarious embodiments, deposited drops 114 can be used to make robustelectrical contact with capillaries or other conduits contacting theareas of hydrophilic features 112, during capillary electrophoresis orother processing. Fluid 116, which again can be an oil, can preventevaporation of deposited drops 114 and other aqueous or immiscibleliquids processed on immersion plate 102.

According to various embodiments in a further regard, and morespecifically, PCR, cycle sequencing, or other processing can beperformed on aqueous volumes 106 in immiscible-fluid-discrete-volumeconduit 104. Sequencing primers that can be used in processing ofaqueous volumes 106 can contain the sulfhydryl group. Hydrophilicfeatures 112 of immersion plate 102 can be made of gold, and bind thesequencing ladders. In view of the fact that the cavity or recess ofimmersion plate 102 is immersed under fluid 116, deposited drops 114 donot evaporate, allowing the gold-thiol bond to form. Immersion plate 102can be washed to remove dye-terminators and salts. Immersion plate 102can then be re-immersed with fluid 116, while retaining analyte with orwithout an aqueous liquid, on hydrophilic features 112. If retainedanalyte is contacted with a fresh fluid, the fresh fluid can containreductant to cleave the gold-thiol bond, as well as make robustelectrical contact with the tips of capillary electrophoresiscapillaries or other intake conduits. Fluid 116 can prevent theevaporation of deposited drops 114 or other aqueous liquids, forexample, fresh fluid and/or injection fluid described herein. Accordingto various further embodiments, reductant is not necessarily required,if the voltage applied during injection is sufficient to reduce thegold-thiol bond. While components of a drop are bound to the surfacethrough a gold-thiol bond, the surface of immersion plate 102 can bewashed, rinsed, or otherwise treated. Then, deionized water can be addedto the spot, with a low concentration of buffer, and in some cases acleaving agent to cleave the thiol-gold bond. Cleavage can also occurthrough the application of voltage to the surface of immersion plate102.

According to various embodiments in a further regard, hydrophilicfeatures 112 can be non-conductive, and bind either amplicon orsequencing ladders through a mechanism other than gold-thiol bonding,such as a streptavidin hydrophilic feature that binds a biotinylatedDNA. If the biotinylated DNA needs to be released later, the biotin cancontain a photocleavable linker. According to various embodiments inthis regard, where the surface of immersion plate 102 is non-conductive,deposited drops lodged on hydrophilic features 112 can be large enoughthat both a capillary and an electrode, or a capillary comprising anelectrode, can contact the deposited drops. In some embodiments,immersion plate 102 can be provided with a temperature control device,for example, resistive heaters, a peltier device, a thermal cycler, orthe like, to enable, for example, cycle-sequencing and/or release ofbound analytes.

According to various embodiments, charge-neutral or positively-chargeddye-terminators can be used for cycle sequencing of aqueous volumes 106.The aqueous volumes 106 so processed can be deposited onto hydrophilicfeatures 112 of immersion plate 102, and directly injected intodownstream capillary electrophoresis or other processes. Hydrophilicfeatures 112 can, in various embodiments, be conducting ornon-conducting. According to various embodiments, the ionic strength ofthe deposited drops 114 can be reduced by pre-loading each hydrophilicfeature 112 with water or other low ionic strength liquid prior todepositing aqueous volumes 106 containing higher ionic strengthsequencing reaction.

In some embodiments, one or more of the hydrophilic features cancomprise a pre-deposited aqueous fluid deposited thereon. Through theforces of surface tension and due to the coalescing nature of aqueoussamples, the pre-deposited aqueous fluid can attract and/or pull animmiscible-fluid-discrete-volume 106, discharged from discharge tip 108,to hydrophilic feature 112, enabling some degree of tolerance withrespect to aligning discharge tip 108 with each hydrophilic feature 112.

FIGS. 4A and 4B are cross-sectional side views of a system that can beused to deposit a desired discrete volume in a well of a sample tray. Asshown in FIGS. 4A and 4B, an inner tube 113, is shown containing aqueousimmiscible-fluid-discrete-volumes separated by one another withnon-aqueous spacing fluid. Inner tube 113 can comprisepolytetrafluoroethylene. According to various embodiments, materialsother than polytetrafluoroethylene can be used to form the inner tube orthe outer tube. The material can comprise, for example, one or more ofsilicone rubber, glass, butadiene rubber, other rubbers, nylon, otherfluoropolymers, or polyethyleneterephthalate.

According to various embodiments, an apparatus is provided comprising afirst conduit exemplified herein as an inner tube, a second conduitexemplified herein as an outer tube, a first pump, and a second pump.The inner tube can comprise a length, an inner surface, an outersurface, an outer diameter, and at least a first end surface, and theouter tube can comprise a length, an inner surface, an inner diameter,an outer surface, and at least a second end surface, wherein the innertube can be positioned within the outer tube and the inner diameter ofthe outer tube is greater than the outer diameter of the inner tube suchthat a fluid can flow in a space between the outer surface of the innertube and the inner surface of the outer tube. The first pump can be influid communication with the inner tube, wherein the first pump isconfigured to flow a fluid through the inner tube in a first direction,and the second pump can be in fluid communication with the outer tube,where the second pump can be configured to flow a fluid through theouter tube in a second direction opposite the first direction. It shouldbe understood that while tubes are exemplified herein, any suitableconduits can instead be used, and the conduits do not have to have anyparticular shape or dimensions. In various embodiments, at various timesthe end surface of the inner tube can be positioned beyond the endsurface of the outer tube. In various embodiments, the outer diameter ofthe inner tube can be less than about 10 mm, less than about 1 mm, orless than 0.1 mm. In other embodiments, the inner diameter of the outertube can be greater than about 10 mm, greater than about 1 mm, orgreater than about 0.1 mm. Regardless of the outer diameter or perimeterof the inner tube, the inner diameter or perimeter of the outer tubewill be greater than the outer diameter or perimeter of the inner tube,such that a fluid passage can be formed in the space between the outertube and the inner tube.

According to various embodiments, the apparatus can comprise a controlunit configured to synchronize actuation of the first pump and thesecond pump. According to various embodiments, the apparatus cancomprise a conduit positioner configured to move at least one of theinner tube and the outer tube with respect to the other. In variousembodiments, the apparatus can comprise a control unit configured tosynchronize actuation of the first pump, the second pump, and theconduit positioner. The synchronized actuation of the pumps and conduitpositioner can result in production of a plurality of aqueousimmiscible-fluid-discrete-volumes, each of which is immiscible with anon-aqueous spacing fluid that separates the aqueousimmiscible-fluid-discrete-volumes from one another. In variousembodiments, the actuation of the pumps and conduit positioner canresult in rinsing the tip of the inner tube between sample liquiddepositing steps, thereby avoiding contamination of a subsequentlydeposited sample liquid with the previously deposited sample liquid. Oneof skill in the art can determine additional patterns of actuation ofthe pumps and the conduit positioner, as well as appropriate pumppressures, to accomplish a desired result.

According to various embodiments, the apparatus can comprise a block inthe form of a housing, shroud, casing, or the like. The block cancomprise a through-hole having a diameter that is greater than the outerdiameter of the inner tube or maximum outer dimension of an innerconduit of a different shape. The block having a through-hole can takethe place of an outer tube and can function as the outer fluid conduit,as shown in FIGS. 30 and 31, or, in another embodiment, can be providedin addition to an inner tube and an outer tube. At least a portion ofthe inner tube can be disposed in the through-hole of the block. Invarious embodiments, an inner conduit, an outer conduit, and a block canall three be included in the apparatus, and the end surface of the outerconduit can be disposed within the through-hole of the block, and/or theend surface of the inner tube can be disposed within the through-hole ofthe block. In other embodiments, the inner conduit can extend beyond theend surface of the outer conduit and beyond the block.

According to various embodiments, the apparatus can comprise a blockhaving a through-hole, and a passageway in the block, the passageway canbe in direct fluid communication with the through-hole as a result ofthe junction of the through-hole and the passageway in the block.According to various embodiments, the apparatus can comprise a pump influid communication with the passageway and configured to draw fluidfrom the conduits in the through-hole and into the passageway. In otherembodiments, the passageway may not be in direct fluid communicationwith the through-hole. Rather the open end of the through-hole and anopen end of the passageway may be in sufficiently close proximity suchthat a fluid from a tube in the through-hole can be sucked into the openend of the passageway. The passageway can lead to or be operativelyconnected to a waste container or other container into which the fluidcan be deposited.

According to various embodiments, a system is provided comprising anapparatus and a supply of oil. In various embodiments, the apparatus canalso comprise a supply of an aqueous liquid, for example, an aqueousbiological sample solution, or other aqueous-based reagents. In variousembodiments, the system can comprise sample liquid disposed in a samplecontainer, and the positioner is configured to move the tip of the innertube into the sample container and into contact with the sample liquid.

According to various embodiments, the method can comprise moving theinner conduit into the outer conduit such that the end surface of theinner conduit and the end surface of the outer conduit are flush orrelatively flush with one another, that is, within one millimeter orless of each other, or such that the end surface of the inner conduitcan be inside the outer conduit. Various embodiments can comprise movingthe end surface of the outer conduit into a through-hole of a block orshroud, such that the end surface of the outer conduit us inside thethrough-hole.

According to various embodiments, the method can comprise rinsing theend surface of the inner conduit with the first fluid, and drawing awayfrom the end surface of the inner conduit the first fluid used to rinsethe end surface of the inner conduit. In various embodiments, the fluidused to rinse the end surface the inner conduit can be flushed through-apassageway of a block. According to various embodiments, the block cancomprise a passageway and the method can comprise drawing the firstfluid used to rinse the end surface of the inner conduit through-thepassageway and away from the through-hole.

According to various embodiments, aqueousimmiscible-fluid-discrete-volumes can be confined between oilimmiscible-fluid-discrete-volumes that can act as a spacer material topreserve individuality of the aqueous immiscible-fluid-discrete-volumes.According to various embodiments, the flow in the tube, channel, orother conduit can be laminar, with a velocity profile along the tube'saxial orientation, with little or no velocity component in the radialdirection.

According to various embodiments, the tip of inner tube 113 can berinsed between aqueous liquid depositing or discharging steps. A suctioncan be directly applied to outer tube 114 or can be applied to anothertube or passageway that is located close to outer tube 114, and/or canbe located in a block 300, as exemplified in FIG. 4B. In someembodiments where a block 300 is used, outer tube 114 can be omitted andthe discharge tip of inner tube 113 can be rinsed off by a liquid thatis vacuumed away through block 300.

FIGS. 4A and 4B illustrate an apparatus that can collect an aqueousliquid by removing an aqueous liquid from a well, and rinse and/or cleanthe tip of the immiscible-fluid-discrete-volume-forming tube. In suchembodiments, an immiscible-fluid-discrete-volume-forming (inner) tubecan be lowered into a well. When the inner tube is lowered into thewell, a pump can discharge fluid from the inner tube into the well. Theinner tube can then be withdrawn from the well, by raising the tubeindividually, by raising the entire apparatus, or by lowering the well.When the inner tube is removed from the aqueous liquid in the well, asolution from outer tube 114 can rinse-off the tip of inner tube 113.For example, oil supplied through outer tube 114 can be used torinse-off the tip of inner tube 113, and the rinse oil can be removedthrough a separate channel. As mentioned above, in some embodimentsouter tube 114 is not used in the system and rinse fluid can be suppliedthrough block 300 and vacuumed away from the discharge tip of inner tube113 also through block 300, in which case block 300 can be provided witha rinse fluid supply conduit and a waste removal conduit.

As shown in FIG. 4A, the apparatus can contain aqueousimmiscible-fluid-discrete-volumes 304 and non-aqueous spacing fluid 306in inner tube 113. Aqueous immiscible-fluid-discrete-volumes 304 ininner tube 113 can be pumped to another portion of the system (asindicated by the arrow at the top of the figure) where processing and/ordisposal of aqueous immiscible-fluid-discrete-volumes 304 and disposalof spacing fluid 306 can occur, for example, as shown in FIG. 6 and FIG.5A, respectively. The aqueous immiscible-fluid-discrete-volumes can bedischarged into a system for a reaction or hybridization, to asubstrate, platform, or container for analysis or further processing, orinto a waste container, as deemed appropriate.

The embodiment shown in FIGS. 4A and 4B depicts both an inner tube 113and an outer tube 114 passing through a through-hole 299 in a block 300.It is to be understood, however, that in some embodiments through-hole299 itself can serve as the outer conduit or outer tube of theapparatus, and in some embodiments a pump can be operatively connecteddirectly to the through-hole 299.

According to various embodiments and as shown in FIG. 4B, block 300 cancomprise a solid block having a through-hole formed therein for innertube 113 and outer tube 114. The block can be made of any number ofdifferent materials. Any suitable material for forming passagewaystherein for fluids and/or for tubes going through the block can be used.The material should not react or should only very minimally react withany fluids flowing through the material. Exemplary materials for block300 and for block 308 described below include plastic,polyethyleneterephthalate, polycarbonate, polytetrafluoroethylene,stainless steel, aluminum, glass, and the like. Surfaces of block 300and block 308 that contact liquids can be coated with an inert,protective, and/or hydrophobic coating. In various other embodiments,block 300 and block 308 can each comprise more than one piece, ratherthan a monolithic block. As shown in cross-section, block 300 cancomprise passageway 301 and tube 302 for directing waste fluids or otherfluids to an appropriate location or container, in some embodiments,passageway 301 and tube 302 can be in fluid communication with a pumpand a waste container. The direction of liquid flow is shown by arrowsin the figure.

Block 300 can have a passageway portion extending therethrough that canpermit er tube 113 and outer tube 114 to pass therethrough. In someembodiments, inner tube 113 can move relative to outer tube 114 andblock 300. In various embodiments, the tubes can remain stationary andblock 300 can move relative to the tubes. In other embodiments, block300 can remain stationary and both tubes move relative to block 300. Invarious embodiments, the arrangement of tubes and block 300 can be movedup and down relative to one or more liquid or sample containers.

In some embodiments, block 300 can be in an “up” position, relative toinner tube 113, as shown in FIG. 4A such that at least inner tube 113extends beyond the edge of block 300, Alternatively, block 300 can be ina “down” position, relative to inner tube 113, as shown in FIG. 4B suchthat the end of inner tube 113 does not extend or only minimally extendsbeyond block 300. The p “down” position can be accomplished either bymoving the tubes relative to block 300, or by moving block 300 relativeto the tubes.

As shown in FIGS. 4A and 4B, when block 300 is in the “up” position, ertube 113 can deposit sample liquid 312 into well 313 of sample tray 310.Inner tube 113 can then be withdrawn into outer tube 114 to permitspacing fluid 319 to rinse the tip of inner tube 113.

When block 300 is in a “down” position as shown in FIG. 4B, the pump influid communication with inner tube 113 can be shut off, and wastesolution can flow through passageway 301 and out waste tube 302. Invarious embodiments, a pump can be in fluid communication with wastetube 302 in order to pump, for example, air and/or excess oil from outertube 114, thereby rinsing contaminants, unwanted sample liquid, and/orreagent from end surface or tip 309 of inner tube 113.

According to various exemplary embodiments, tip 309 of inner tube 113can be placed appropriately to discharge sample liquid 312 in well 313of sample tray 310. Exemplary sample trays can comprise microtiterplates, picotiter plates, 24-well plates, 96-well plates, 384-wellplates, 1536-well plates, 6144-well plates, plates with removable samplevials, a card-type assay device, a flat surface, and array of vials, andthe like. The pump that is operatively connected to, and in fluidcommunication with, inner tube 113 can dispense aqueous liquid throughtip 309 and into a well or onto a plate situated thereunder. Tip 309 ofinner tube 113 can thereafter be withdrawn from in or near the well orplate. Withdrawal of tip 309 of inner tube 113 can be accomplishedeither by raising inner tube 113 into outer tube 114, resulting in theillustration shown in FIG. 4B, or by raising the entire apparatus 100away from the sample.

When inner tube 113 is in the position shown in FIG. 4B, oil or anotherspacing fluid flowing out of outer tube 114 can rinse-off the endsurface or tip of inner tube 113. The spacing fluid used as the rinseliquid can then be directed through passageway 301 in block 300 and becarried away to a waste station (not shown) operatively connected towaste tube 302. In some embodiments, a pump 380 (see FIG. 4A) can beconnected to waste tube 302. In various embodiments (not shown) theentire length of passageway 301 can accommodate a tube such that block300 has a liner therein for passageway 301. The positioning of the tubesrelative to block 300 can be accomplished by keeping block 300 in asingle position and moving the tubes relative to block 300, or by movingblock 300 relative to the tubes, or by a combination of the two types ofmovements.

As shown in FIG. 4A, in some embodiments a control unit 350 can beprovided that can independently control a plurality of pumps 360, 370,380, for respectively flowing fluids through first conduit 113, secondconduit 114, and waste tube 302. Pump 370 can be operatively connectedto outer conduit 114 through a tube 121 connected to block 308.

As shown in FIGS. 4A, 4B, 5A, and 5B, apparatus 100 can comprise shroudor block 300 and a second block 308. Block 308 can form a structure thatassists in supporting inner tube 113 and/or outer tube 114. Block 308can comprise a through-hole passageway for inner tube 113 and for outertube 114, or block 308 can comprise appropriate connections or bores toattach conduits such as capillary tubes to the block. The passageway cancomprise an elbow 314 and openings 316 and 320 (See FIG. 5B). It will berecognized that the point of entry of inner tube 113 into outer tube 114can be sealed to keep the contents of outer tube 114 from leaving outertube 114 or block 308. Sealing can be accomplished with appropriateboring and/or counter-boring, and/or using a sleeve, bearing, sealinggasket, O-ring, or the like, where appropriate.

According to various embodiments, elbow in block 308 does notnecessarily contain outer tubing 114. Instead, outer tubing 114 can beconnected to block 308 via an appropriate connection, for example, via abore 330 in block 308. At opening 320, outer tube 114 can also beconnected such that fluid can move from outer tube 114, into block 308,and into tube exiting block 308. Thus, only inner tube 113 actuallypasses through block 308 in the embodiment depicted.

In order to accomplish a desired result, for example, rinsing the tip oftubes used for discharging volumes of sample liquid, a control unit 350(see FIG. 4A) can be used for regulating appropriate flow rates andappropriate starting and stopping of the pumps in fluid communicationwith inner and outer tubes. Such a controller can control an actuatorfor turning the pumps on and off as desired. The controller can comprisea computer. Appropriate pump speeds and actuations of the pumps can bedetermined to accomplish the removal of waste from the tip of inner tube113.

According to various embodiments, a method is provided that comprises:pumping a first fluid in a first direction in a space between an outerperimeter of a first conduit and an inner perimeter of a second conduit;drawing the first fluid past an end surface of the first conduit, andinto the first conduit in a second direction that is opposite the firstdirection; and positioning the first conduit into a receptaclecontaining a second fluid that is immiscible with the first fluid, anddrawing at least a portion of the second fluid past the tip of the firstconduit. In some embodiments, the method further comprises, beforepositioning into the receptacle, positioning at least one of an endsurface of the first conduit and an end surface of the second conduitsuch that the end surface of the first conduit is beyond the end surfaceof the second conduit. In some embodiments, the method comprises, afterdrawing at least a portion of the second fluid, positioning at least oneof the first conduit and the second conduit such that the end surface ofthe first conduit can either be flush with the end surface of the secondconduit or inside the second conduit. In some embodiments, the secondconduit can comprise a block having a through-hole, and positioning atleast one of the first conduit and the second conduit can comprisemoving the end surface of the first conduit into the through-hole. Insome embodiments, the method can further comprise drawing at least aportion of the second fluid past the tip of the first conduit to rinsethe end surface of the first conduit with the first fluid.

According to various embodiments, waste, for example, spacing fluidbetween adjacent sample immiscible-fluid-discrete-volumes, can beremoved. As the spacing fluid comes out of the tip 309 of inner tube113, outer tube 114 can have a suction applied to it and any unwantedspacing fluid sample immiscible-fluid-discrete-volumes can be removed.

FIGS. 5A and 5B illustrate an embodiment for removing waste from aninner tube 113 and/or for depositing desired samples in a container. Forsuch a usage the apparatus can be placed at the back-end of a system,such that already prepared immiscible-fluid-discrete-volumes can be“spit out” from the inner tube and waste can be sucked away through theouter tube. In such usage, pumping of immiscible-fluid-discrete-volumesand/or other solutions can occur in different directions than shown inFIGS. 4A and 4B. In various embodiments, the apparatus can first be usedto obtain sample immiscible-fluid-discrete-volumes spaced from oneanother by spacing fluid, and then a similar apparatus on the back-endof the system can have reverse pump directions such that sampleimmiscible-fluid-discrete-volumes and/or spacing fluid can be “spit out”either collected or sent to a waste receptacle.

In the “up” position shown in FIG. 5A, waste can be sent to a wastecontainer. In the down position shown in FIG. 5B, a desired sampleimmiscible-fluid-discrete-volume can be deposited in a desiredcontainer. In the down position, suction normally being applied to outertube 114 can be stopped or sufficiently slowed down such that thedesired sample immiscible-fluid-discrete-volume can be deposited in anappropriate sample well.

According to various embodiments, the downstream processes can becarried out in a capillary channel, for example, a capillary tube. Thecapillary tube can be in fluid communication with apparatus 100 as shownin FIG. 6. An exemplary capillary tube that can be used can have aninner diameter of about 1000 microns or less. In other embodiments theinner diameter can be about 300 microns or less, for example, about 100microns or less, or about 50 microns or less. Other embodiments caninvolve methods that use a capillary tube having an inner diameter thatis greater than about 300 microns, for example, from about 500 micronsto about 1000 microns, or about 500 microns or less. In variousembodiments, the above dimensions can refer to the maximumcross-sectional dimension of the capillary channel. Such a channel canbe rectangular in shape or have any other suitable shape. Varioussystems and apparatus can also be provided that include such a capillarychannel.

FIG. 6 illustrates a system that can use one or more embodiments ofapparatus 100. In various embodiments, aqueousimmiscible-fluid-discrete-volumes spaced apart by spacing fluid areprepared in apparatus 100. A pump 160, control unit 165, pump 180,control unit 185, spacing fluid source 190, can be used to prepare theaqueous immiscible-fluid-discrete-volumes. The aqueousimmiscible-fluid-discrete-volumes can then also be pumped to the rest ofthe system 200 with pump 160. The rest of the system represented by theblack box designated 200 can comprise a system as shown and described inU.S. Provisional Patent Application No. 60/710,167, filed Aug. 22, 2005,which is incorporated herein in its entirety by reference, or any of theimmiscible-fluid-discrete-volume processing systems described and shownherein. A pump 210 can be operatively connected to waste tube 208. Pump210 can be controlled by a control unit 215, and control unit 215 can beoperatively connected to one or more other control units in the system.

In some embodiments, a method is provided that can comprise using thesystem described herein to process an aqueousimmiscible-fluid-discrete-volume. According to various embodiments, themethod can comprise amplifying at least one target nucleic acidsequence, for example, in a processing conduit downstream of theimmiscible-fluid-discrete-volume-forming inner conduit described above.According to various embodiments, the method can comprise introducingpolymerase chain reaction inactivating reagents into a processingconduit, for example, a capillary channel, after amplifying the at leastone target nucleic acid sequence and before subjecting the nucleic acidsequence to a sequencing reaction. The reagents can be used toinactivate or remove or eliminate excess primers and/or dNTP's resultingfrom or leftover from an amplification process. The inactivatingreagents can be introduced at a junction in the processing conduit, forexample, after an aqueous sample immiscible-fluid-discrete-volume to beinactivated is aligned with the junction. The junction can comprise, forexample, a T-intersection or a Y-intersection.

According to various embodiments, one or more target nucleic acidsequences can be subjected to a sequencing reaction to form a detectableproduct, and the method can comprise detecting the detectable product.In various embodiments, the detectable product can be detected insidethe same processing conduit or capillary channel where the detectableproduct is formed. In other embodiments, the detectable product can betransferred out of the processing conduit and detected using, forexample, using a flow cell or a capillary electrophoretic sequencer. Invarious other embodiments, an off-capillary detector can be used asdeemed appropriate.

FIG. 7 illustrates the injection of charged analytes from processedimmiscible-fluid-discrete-volumes into a downstream, capillaryelectrophoresis intake tip, according to various embodiments of thepresent teachings. According to various embodiments as shown in FIG. 7,an immiscible-fluid-discrete-volume output conduit 702 can contain asequence of aqueous volumes 704, such as liquid samples, separated byspacing fluid 706. Spacing fluid 706 can be, for example, oil or otherliquid that is immiscible with aqueous volumes 704.Immiscible-fluid-discrete-volume output conduit 702 can be positionedadjacent, and in contact or abutted with, a capillary electrophoresiscapillary 708. Capillary electrophoresis capillary 708 can be filledwith separation medium 726, such as acrylamide gel or other separationor sieving medium for separating the contents of aqueous volumes 704 byelectrophoresis. According to various embodiments as shown in FIG. 7,aqueous volumes 704 can be generated and/or processed by varioustechniques described in co-pending U.S. patent application Ser. No.______, filed Aug. 22, 2006, entitled “Device and Method for MakingDiscrete Volumes of a First Fluid in Contact with a Second Fluid Whichare Immiscible with Each Other” to Cox et al. (attorney docket number5010-363), which is incorporated herein in its entirety by reference,and be or include biological material such as DNA samples combined withprimer and other reagents. According to various embodiments as shown inFIG. 7, aqueous samples 704 can be injected into capillaryelectrophoresis capillary 708 by direct pressure injection, for instanceby closely positioning an output end of immiscible-fluid-discrete-volumeoutput conduit 702 against capillary electrophoresis capillary 708, andapplying pressure and/or vacuum to drive and/or pull aqueous samples 704into the tip of capillary electrophoresis capillary 708 and intoseparation medium 726. DNA or other sample material of interest can thenbe separated, identified, sequenced, or otherwise processed byelectrophoretic separation in separation medium 726.

As shown in FIG. 8A, according to various embodiments, animmiscible-fluid-discrete-volume output conduit 710 can contain a set ofaqueous volumes 718, such as samples, separated by spacing fluid 720,such as oil or other liquid that is immiscible with aqueous volumes 718.According to embodiments as shown in FIG. 8A, the output end ofimmiscible-fluid-discrete-volume output conduit 710 can be positionedadjacent to, and in contact or abutted with, a set of capillaryelectrophoresis capillaries 714, each of which is filled with separationmedium 726, such as acrylamide gel or other sieving or separationmedium. According to various embodiments as shown in FIG. 8A,immiscible-fluid-discrete-volume output conduit 710 can be movablypositioned to be axially aligned with a selected one or more ofcapillary electrophoresis capillaries 714. According to variousembodiments, aqueous volumes 718 can be injected into the tip of therespective one of capillary electrophoresis capillaries 714 with whichimmiscible-fluid-discrete-volume output conduit 710 is aligned.According to various embodiments, injection of aqueous volumes 718 canbe performed by pressure injection and/or vacuum.

According to various other embodiments as shown in FIG. 8A, aqueousvolumes 718 can be injected into a tip of the respective one ofcapillary electrophoresis capillaries 714, with whichimmiscible-fluid-discrete-volume output conduit 710 is aligned, forexample, axially aligned, by electrokinetic injection. According toembodiments as shown, immiscible-fluid-discrete-volume output conduit710 can be provided with immiscible-fluid-discrete-volume conduitelectrode 712, while each of capillary electrophoresis capillaries 714can be provided with capillary electrophoresis capillary electrode 716.

As shown in FIG. 8B, capillary electrophoresis capillary electrode 716can be formed as an annular cladding that surrounds an outercircumference of capillary electrophoresis capillaries 714. According tovarious embodiments, capillary electrophoresis capillary electrode 716can be formed by electroplating, vapor deposition, or can be formed as aseparate electrode element, such as a sheath fitted to capillaryelectrophoresis capillaries 714, that again can contain separationmedium 726. According to various embodiments,immiscible-fluid-discrete-volume conduit electrode 712 can be formed ina similar or same manner as capillary electrophoresis capillaryelectrode 716. According to various embodiments, an electric potentialcan be applied between immiscible-fluid-discrete-volume conduitelectrode 712 and an electrode at an opposite end of the capillaryelectrophoresis capillary relative to the end shown, to perform anelectrokinetic injection from aqueous volumes 718 into the respectivecapillary electrophoresis capillaries 714. According to variousembodiments, an electric potential or field can be generated accordingto other electrode configurations, for example to provide the same ordifferent electric potential between each ofimmiscible-fluid-discrete-volume conduit electrode 712 and capillaryelectrophoresis capillary electrode 716 and ground. According to variousembodiments, either direct current, alternating current, or acombination of direct and alternating current can be applied to eitherof immiscible-fluid-discrete-volume conduit electrode 712 and capillaryelectrophoresis capillary electrode 716. According to variousembodiments, one or more than one power supply can be used to applyelectric power to immiscible-fluid-discrete-volume conduit electrode 712and capillary electrophoresis capillary electrode 716.

As shown in FIGS. 7, 8A, 8B, and 9, according to various embodiments ofthe present teachings, aqueous volumes 734 can be injected from animmiscible-fluid-discrete-volume conduit 728 into a tip of a capillaryelectrophoresis capillary 736 by electrokinetic injection. According tovarious embodiments, capillary electrophoresis capillary 736 can containseparation medium 726. In some embodiments as shown conduit 728 can beprovided with immiscible-fluid-discrete-volume conduit electrode 730,while capillary electrophoresis capillary 736 can also be provided withcapillary electrophoresis capillary electrode 738.

According to various embodiments, capillary electrophoresis capillaryelectrode 738 can be formed as an annular cladding that surrounds anouter circumference of capillary electrophoresis capillary 736. In someembodiments, capillary electrophoresis capillary electrode 738 can beformed by electroplating, vapor deposition, or can be formed as aseparate electrode element, such as a sheath fitted to capillaryelectrophoresis capillary 736. In some embodiments,immiscible-fluid-discrete-volume conduit electrode 730 can be formed ina similar or same manner as capillary electrophoresis capillaryelectrode 716. According to various embodiments, an electric potentialcan be applied between immiscible-fluid-discrete-volume conduitelectrode 730 and a capillary electrophoresis capillary electrode at anopposite end of the capillary relative to the end where electrode 738 toperform an electrokinetic injection from aqueous volumes 734 intocapillary electrophoresis capillary 736. In some embodiments, otherelectrode configurations can be used, for example to provide the same ordifferent electric potential between each ofimmiscible-fluid-discrete-volume conduit electrode 712 and capillaryelectrophoresis capillary electrode 716 and ground.

According to various embodiments, either direct current, alternatingcurrent, or a combination of direct and alternating current can beapplied to either of immiscible-fluid-discrete-volume conduit electrode712 and capillary electrophoresis capillary electrode 716 from one ormore than one electric power supply.

In some embodiments, each of electrodes 712, 730, 740, and 760, forexample, can independently comprise a pin electrode.

According to various embodiments as shown in FIG. 9, the injection ofaqueous volumes 734 can likewise be augmented by dielectricconcentration. More specifically, according to embodiments as shown inFIG. 9, electrodes 740 can be provided in a generally opposedconfiguration near the intake tip of capillary electrophoresis capillary736. According to various embodiments, electrodes 740 can beelectrically connected to a power supply 742 that delivers alternatingcurrent at the tip area of capillary electrophoresis capillary 736 toinduce a dielectrophoretic effect acting on aqueous volumes 734.According to embodiments of the present teachings in this regard, thesalt concentration and other properties of aqueous volumes 734 inimmiscible-fluid-discrete-volume conduit 728 resulting from cyclesequencing, polymerase chain reaction (PCR), or other processing can bemaintained without adversely affecting the amount of aqueous volumes 734injected into capillary electrophoresis capillary 736. According tovarious embodiments as shown in FIG. 9, dielectric concentration can beachieved by maintaining immiscible-fluid-discrete-volume conduit 728 andcapillary electrophoresis capillary 736 in axial alignment in closeproximity as shown, and maintaining most of the emerging volume or slugof aqueous volumes 734 in immiscible-fluid-discrete-volume conduit 728.An AC electric field can then be applied via electrodes 740 toconcentrate DNA or other material of interest in the emerging volume ofaqueous volumes 734 by dielectrophoretic action. Better separation,detection and other electrophoresis characteristics can in one regardthereby be achieved. In some embodiments electrodes 730 and 738 can beused to perform concentration, rendering electrode 740 optional.

According to various embodiments as shown in FIGS. 10A and 10B, theinjection of aqueous volumes 754 can similarly be augmented bydielectric concentration, and also enhanced by introducing a delaybefore injection. More specifically, according to embodiments as shownin FIG. 10A, electrodes 760 can be provided in a generally opposedconfiguration near the intake tip of capillary electrophoresis capillary756. Capillary electrophoresis capillary 756 can be provided withelectrodes 758, for example, annular electrodes for electrokineticinjection. Capillary electrophoresis capillary 756 can be generallyaligned, for example, axially, with an immiscible-fluid-discrete-volumeconduit 750 in which aqueous volumes 754 can be contained, separated byspacing fluid 756, such as oil or other liquid. According to variousembodiments, electrodes 760 can be electrically connected to a powersupply 762 that delivers alternating current at the tip area ofcapillary electrophoresis capillary 756 to induce a dielectrophoreticeffect acting on aqueous volumes 754. According to embodiments of thepresent teachings in this regard, the salt concentration and otherproperties of aqueous volumes 754 in immiscible-fluid-discrete-volumeconduit 750 resulting from cycle sequencing, PCR, or other processingcan be maintained without adversely affecting the amount of aqueousvolumes 754 injected into capillary electrophoresis capillary 756.

According to various embodiments as shown in FIG. 10A, dielectricconcentration can be achieved by maintainingimmiscible-fluid-discrete-volume conduit 750 and capillaryelectrophoresis capillary 756 in axial alignment in close proximity asshown, and maintaining most of the emerging volume or slug of aqueousvolumes 754 in immiscible-fluid-discrete-volume conduit 750. Accordingto embodiments as shown in FIG. 10A, the emerging volume of aqueousvolumes 754 can be maintained in the interstitial area betweenimmiscible-fluid-discrete-volume conduit 750 and capillaryelectrophoresis capillary 756 for a predetermined period of time, toeffect diffusion of DNA or other sample material in the emerging volume.The time period can be after dielectrophoretic concentration, whichbrings all the small and large molecules of DNA initially together. At aperiod of time shown in FIG. 10A, smaller DNA molecules or fragments,ions, or other material can be intermingled with larger and slower DNAmolecules and other heavier, larger, or slower fragments in the emergingaqueous volume. A period of time, for example, on the order of severalseconds, or more or less time, can be permitted to elapse. After thedelay, the components of the emerging volume of the aqueous volumes 754migrate or diffuse to separate regions, leaving primarily larger, slowerDNA molecules or fragments, larger ions, or other larger, heavier, orslower components grouped closer together at the leading edge of theemerging aqueous volume. As shown in FIG. 10B, an AC electric field canthen be applied via electrodes 760 to concentrate DNA or other materialof interest in the emerging volume of aqueous volumes 754 bydielectrophoretic action, for example, before diffusion caused byelectrokinetic injection. The dielectrophoretic action applied to anaqueous volume whose components have already partially separated bydiffusion, even further improved separation, detection and otherelectrophoresis characteristics can in one respect thereby be achieved.After dielectrophoretic concentration, the sample can be injected byelectrokinetic injection.

As shown in FIG. 10C, an aqueous volume is emerging into a gap betweenconduit 750 and capillary 756. In some embodiments, electrodes can bedisposed in the gap. In some embodiments, electrodes 770 can penetratethe wall of conduit 750 and electrically connect to an annular,two-part, ring electrode inside conduit 750. Electrodes 760 can beconfigured close to capillary electrophoresis capillary 756, but withouta necessity that the emerging aqueous volume of aqueous volumes 754 bemaintained in immiscible-fluid-discrete-volume conduit 750. According toembodiments as shown, the gap between immiscible-fluid-discrete-volumeconduit 750 and capillary electrophoresis capillary 756 can beconfigured as a cross channel, into which spacer fluid 756, and most ofthe emerged immiscible-fluid-discrete-volume, can be removed and flowedaway prior to and/or during the injection process. Concentrated chargedanalytes can migrate into capillary electrophoresis capillary 756 andconsequently avoid being washed away. According to various embodiments,the cross channel can also receive a wash solution to clean the tips ofimmiscible-fluid-discrete-volume conduit 750 and/or capillaryelectrophoresis capillary 756. Discussion of injection across a gap asillustrated can be found, for example, U.S. Pat. No. 5,110,431 to Moringet al. and U.S. Pat. No. 5,798,032 to Khan et al., each of which isincorporated by reference in its entirety herein.

In some embodiments, electrodes 712, 716, 730, 738, 770, 752, 758, andthe like can be formed by vapor deposition, for example, to coat the endsurface of the respective conduit or capillary, and in some cases, toform an electrode coating on an inner surface thereof.

According to various embodiments in another regard, if the emergingaqueous volume is small enough, such that the injected aqueous volumedoes not significantly increase the size of a detected peak afterelectrophoresis, the injected aqueous volume can be directly injectedinto capillary electrophoresis capillary 756 by direct pressureinjection, by pushing the aqueous volume into capillary electrophoresiscapillary 756 from immiscible-fluid-discrete-volume conduit 750positioned adjacent thereto. According to various embodiments in anotherregard, if the emerging aqueous volume if large enough to adverselyaffect detected peak size after electrophoresis, dielectrophoreticconcentration can be performed in capillary electrophoresis capillary756, as for example described in U.S. Pat. No. 6,537,433 to Bryning etal, which is incorporated herein by reference in its entirety. Accordingto embodiments of the present teachings in another regard, if the saltconcentration is determined to be high in aqueous volumes 754, deionizedwater can be added to aqueous volumes 754 to reduce salt concentration.According to various embodiments in a further regard, adi-electrophoretic concentration can be performed at the end ofimmiscible-fluid-discrete-volume conduit 750, prior to pressureinjection or electrokinetic injection into capillary electrophoresiscapillary 756.

As illustrated in FIG. 11, a sample can be deposited on electricallyconductive surface 1108 of a sample apparatus 1120. Sample apparatus1120 can comprise substrate 1104, and a layer 1102 that can make-up, inwhole or in part, electrically conductive surface 1108. In variousembodiments, substrate 1104, itself, can be the electrically conductivematerial, for example, gold that can have electrically conductivesurface 1108. In other embodiments, a coating or thin layer 1102 ofelectrically conductive material can form or be part of the conductivesurface.

In some embodiments, an electrically conductive surface is provided thatis coated with a hydrophobic material, for example, a fluoropolymericmaterial, in regions where it is desired to avoid wetting-out orhydrophilic attraction of aqueous sample drops or volumes. In someembodiments, the surface can be generally hydrophobic except in areasspotted with a gold surface material, such that separated electricallyconductive spots or regions can be independently controllable, that is,such that the different spots can be independently made to be inelectrical communication with a voltage source. In some embodiments, agrid, array, or other grouping of spots, regions, areas, or otherlocations can be provided on a surface wherein electrical potentials canbe independently applied to the spots. In some embodiments, a potentialcan be applied to some spots while not being applied to other spots.

In some embodiments, such an array of spots or locations, whetherindependently controllable or not, can be arranged in the same shape andwith the same spacing as the injector tips of an injector array of aprocessing device, for example, to interface with the injector tips of amulti-capillary capillary electrophoresis apparatus. In someembodiments, liquid drops corresponding toimmiscible-fluid-discrete-volumes deposited on an electricallyconductive surface can be arranged on the surface in an array that caninterface with an injector of a two-capillary, four-capillary,eight-capillary, 16-capillary, 48-capillary, or 96-capillary capillaryelectrophoresis apparatus. For example,immiscible-fluid-discrete-volumes to be further analyzed can bedeposited in an 8 by 12 array corresponding to the footprint of astandard 96-well microtiter plate, and all 96 volumes can besimultaneously electrophoretically injected into a 96-capillarycapillary electrophoresis apparatus, for example, a 3730xlmulti-capillary electrophoresis analyzer available from AppliedBiosystems, Foster City, Calif.

The independently controllable electrically conductive spots and/or thearrangement of volumes in an array, as described above, can also beimplemented in various other embodiments of the present teachings,including, for example, the embodiments shown in FIGS. 2, 3, 12-18, 22A,and 22B.

Electrically conductive surface 1108 can receive sample from end or tip1186 of processing channel 1140. The samples can be prepared in a samplepreparation device that is in fluid communication with conduit 1140. Invarious embodiments, conduit 1140 can be a capillary tube. Other typesof conduits, however, can also be used. Discrete volumes 1130, forexample, of a processed aqueous sample, are disposed in conduit 1140 andare spaced apart by spacing fluid 1132, as described herein. Thediscrete volumes 1130 can be prepared in sample preparation device (See,FIGS. 1A and 1B for additional details) and can be deposited ordispensed onto electrically conductive surface 1108 from tip 1186. Invarious embodiments, electrically conductive surface 1108 can comprise,for example, an electrically conductive film or an electroplated layerof a conductive material.

According to various embodiments, sample apparatus 1120 can comprise anidentifier 1114, for example, a bar code, RFID or other identifyinglabel, tag, or indicia. The identifier can assist in quality control orinventory of sample apparatus 1100 or can be used for keeping track ofsamples deposited on sample apparatus 1100. The identification can bemachine readable.

According to various embodiments, electrically conductive surface 1108can be covered with an insulating layer. In such an embodiment,substrate 1104, electrically conductive surface 1108 and the insulatingsurface can act as a capacitor. A sample dispensed onto the surface ofsubstrate 1104 can be injected into a conduit, capillary tube, orchannel from the insulating layer when the substrate acts as acapacitor.

Discrete Volumes 1130 comprising samples of interest and spacing fluid1132 can be pumped from tip 1186 onto electrically conductive surface1108. The spacing fluid can comprise an oil or other liquid that allowsthe spacing fluid to provide a spacing or partitioning portion betweenadjacent aqueous immiscible-fluid-discrete-volumes. Theimmiscible-fluid-discrete-volumes can be dispensed onto electricallyconductive surface 1108 in a controlled pattern or manner, for example,a zig-zag or raster pattern. In various embodiments, alternating spotsdeposited from tip 1186 of conduit 1140 can comprise aqueous samplespots alternating with spacing fluid spots deposited on electricallyconductive surface 1108. In other embodiments, a plurality of spots onelectrically conductive surface 1108 can be aqueous sample spots. Insome embodiments, the plurality of spots can all comprise aqueous samplespots, if prior to deposition on electrically conductive surface 1108,the spacing fluid is diverted to a waste container (See, FIGS. 1A, 1B,and 12 for additional details). In some embodiments, the aqueous samplespots can be deposited in an array adapted to interface with an injectorarray of an analyzer, for example, a capillary electrophoresisapparatus. In some embodiments, plural aqueous sample spots can becombined together into a larger spot, for example, combined in a well,and a multiplexing capillary electrophoresis analysis can then beperformed on the larger spot.

Conduit 1140 can connect to and can be controlled by sample collectiondevice drive arm 1194 and conduit holder 1184 that can together positiontip 1186 in a first position, a second position, or additionalpositions. Control drive arm 1194 and drive unit 1196 can be controlled,for example, by a computer in order to move conduit 1140 in an X and/orY and/or Z direction, as deemed appropriate.

As illustrated in FIG. 12, where reference numerals that are the same asin FIG. 11 represent like components, aqueous sample discrete volumes1130 separated by spacing fluid 1132 can be prepared using animmiscible-fluid-discrete-volume sample preparation device 1267, or asdescribed, for example, in connection with FIGS. 1A and 1B herein. Inthe simplified illustration shown in FIG. 12, sample preparation device1267 can comprise an aqueous sample injection unit 1274, a spacing fluidinjection unit 1276, conduits 1229 and 1231, and conduit junction 1242.Sample injection units 1274 and 1276 can comprise, for example, pumps.Sample preparation device 1267 can comprise a control unit 1266, forexample, comprising a computer, adapted to flow aqueous sample 1130 andspacing fluid 1132 from their respective injection units. Control unit1266 can be adapted to inject volumes of aqueous solution and spacingfluid to form immiscible-discrete-volumes of the aqueous sample inconduit 1140. In various embodiments, control unit 1266 can merelycontrol a conduit junction, for example, junction 1242, or it cancontrol a rotary valve or other valve, and pumps, as described herein.Control unit 1266 can comprise a computer that can be adapted toregulate injection units 1276 and 1274.

According to various embodiments, slugs or other discrete volumes of theaqueous sample can be prepared at a junction by applying a fixedpressure to aqueous sample and spacing fluid that are in conduits 1229and 1231, respectively. Discrete volumes of the aqueous sample can formwith a size and speed that is a function of the conduit, junctiondiameter, pressure for each fluid, and/or viscosity of each fluid.

Discrete volumes of the aqueous sample can be formed by pumping spacingfluid and aqueous sample into conduits 1230 and 1232, respectively. Thenon-aqueous spacing fluid can comprise an oil, for example, afluorocarbon oil. Non-aqueous spacing fluid 1231 is pumped from spacingfluid injection unit 1276 into conduit 1230 and aqueous sample 1229 ispumped from pump 1274 into conduit 1232. Pumps can comprise servomotors,syringes, piston pumps, and/or the like. A valve, for example, valve1235 can be inserted into the system to regulate flows of liquids.Additional valves can be inserted into the system as deemed appropriate.In various embodiments, the aqueous sample does not necessarily comprisea sample because the sample can be added through inlet ports downstreamfrom junction 1242, and instead, the liquid designated 1229 can compriseanother aqueous liquid, for example, containing reactants to react withan aqueous sample downstream.

According to various embodiments, a nucleic acid sample can beamplified, for example, a DNA sample, to form amplicons, in athermo-cycler 1250. In various embodiments, aqueous slugs 1230comprising a DNA sample can be amplified in thermo-cycler 1250 along asection of conduit 1140. Coiling of conduit 1140 in thermo-cycler 1250is merely represented as a section of the conduit that can be used forthermal cycling. Coiling is not mandatory and any arrangement adaptedfor thermocycling can be used. Other arrangements of conduit 1140 canserve equally well to regulate the temperature of the discrete volumesduring reactions. In various embodiments, a length of conduit 1140 canbe an integral part of thermo-cycler 1250.

Valve 1235 can control flow to thermo-cycler 1250. Such valves, however,can be used elsewhere in the system as deemed appropriate. Thetemperature of thermo-cycler 1250 can be maintained or changed as deemedappropriate using a temperature controlled environment (not shown). Thetemperature controlled environment can be produced by direct contact ofthe thermo-cycler 1250. In various embodiments, the temperaturecontrolled environment can be produced indirectly. In other words, bynot making direct contact with thermo-cycler 1250, for example, with anincubator, oven or refrigerator. Thermal regulation of the contents ofconduit 1140 shown in thermo-cycler 1250 can be used in any process ormethod that requires temperature control of samples in partitionedvolumes, for example, in PCR. Additional variations of the system forsample preparation, thermal cycling and slug preparation can be found inU.S. Provisional Patent Application No. 60/710,167 entitled “SamplePreparation for Sequencing” to Lee et al., filed Aug. 22, 2005 (AttorneyDocket No. 5841P), which is incorporated herein in its entirety byreference.

During thermocycling, or at other times in the method, or at variouslocations in the system, an intercalating dye, for example, SYBR greencan be added to a reaction mixture in aqueousimmiscible-fluid-discrete-volumes 1230. Alternatively, the dye can beadded before sample addition to the aqueous slugs. After thermocycling,the aqueous slugs comprising SYBR green can exhibit increasedfluorescence due to the intercalating dye, that is, intercalation of thedye can provide an indication that the PCR was positive, which can inturn indicate that a target molecule was present and amplified. Lack ofthe intercalated dye and/or fluorescence can be used as a basis forexcluding an aqueous immiscible-fluid-discrete-volume from the next stepin a process, thereby saving expensive consumable reagents.

Referring again to FIG. 12, selected discrete volumes can be dispensedonto sample apparatus 1200. As shown, thermo-cycler 1250 can connectdownstream to a sample collection device drive arm 1194. Drive arm 1194and conduit holder 1184 can together position conduit tip 1186 in afirst position, a second position, and/or additional positions andprovide movement in the X and/or Y and/or Z direction. Drive arm 1194,conduit holder 1184, and drive unit 1196 can together comprisecomponents of a collection device 1241. Collection device 1241 canfurther comprise an excitation source 1260 and a detector 1295 that canprovide control signals to control drive arm 1194 and drive unit 1196.Excitation source 1260 can comprise, for example, any of a variety ofillumination sources if detector 1295 comprises a spectrophotometricdetector. Detector 1295 can comprise, for example, a photomultipliertube (PMT), photodiode, and/or a charge coupled device (CCD), or thelike. Detector 1295 can serve several functions, for example, it canassist in determining where samples have been dispensed onto sampleapparatus 1200. In various embodiments, detector 1295 can interact withor control a discriminating device 1262 that enables unwanted samples tobe diverted to a waste container and can control placement of samplesinto desired locations on the plate. Unwanted samples can be aspirated,for example, through tube 1264 of discriminating device 1262, and sentto a waste collector of discriminating device 1262.

At a first position; tip 1186 of conduit 1140 can be positioned so thatdiscrete volumes expelled therefrom can be dispensed onto electricallyconductive surface 1272 of sample apparatus 1200. Additional details ofsample apparatus 1200 can be seen in FIG. 11 in connection with thedescription of sample apparatus 1120.

At a next position, the process is repeated and another spot isdispensed. According to various embodiments, sample apparatus 1200 canbe moved by carriage unit 1290 and drive unit 1292 relative to conduit1140 and/or tip 1186 thereof. As such, a desired pattern of dispensedsample can be provided. In some embodiments, sample apparatus 1200 canbe moved by carriage unit 1290 and drive unit 1292 for furtherprocessing of the dispensed samples.

According to various embodiments, the system can be used in a methodthat can comprise denaturing an attached double-stranded amplicon toform an attached single-stranded amplicon prior to detecting theattached amplicon or an attached derivative thereof, in the at least oneconduit. In various embodiments, the method can comprise reacting theattached single-stranded amplicon with a label prior to detecting theattached amplicon or an attached derivative thereof, in at least oneconduit. The label can comprise a fluorescent or reporter dye, anintercalating dye, a radioactive label, a nano-barcode label or anothertype of marker. An intercalating dye can comprise, for example, SYBRgreen and can be used to identify whether or not a slug comprises anucleic acid sequence. In various embodiments, a label can be used todetect an amplicon, reaction products other than an amplicon, or otherreagents used in the methods and systems.

According to various embodiments, target samples can be preparedcomprising, for example, A and B primers, SYBR green dye and apolymerase. The target samples can be diluted by limiting dilution to asingle molecule per given volume. SYBR green, as well as other dyesknown in the art can be used, as deemed appropriate, at various times inthe process in order to generate a fluorescent signal to be detected.SYBR green and other dyes can produce a change in fluorescent signalupon interacting with double-stranded nucleic acids, thereby permittingthe quantitative or qualitative detection of an amplicon in a slug ofinterest. Such information about the presence, absence, or quantity ofan amplicon in a slug can be used to determine if further analysis ofthe slug is desired. Target samples can be loaded into a conduit in theform of aqueous slugs that are separated from one another by oil slugs.An amplification of target samples can occur within aqueous slug 1130 ina thermo-cycler 1250. In various embodiments, after flowing fromthermo-cycler 1250 following amplification, the target samples can beflowed past a detector. In order to avoid unnecessary waste of expensivereagents, target samples can be flowed past a detector at one or more ofseveral different points in the system and if sample is not present (forexample, as indicated by lack of SYBR green fluorescence), the slugs canbe diverted to a waste container. Examples of such diversion systems canbe found in more detail in the U.S. Provisional Patent Application No.60/710,167 entitled “Sample Preparation for Sequencing” of Lee et at,filed Aug. 22, 2005 (Attorney Docket No, 5841P), incorporated in itsentirety herein by reference. Those aqueous slugs comprising anamplified target sample, for example, those samples fluorescing due toincorporation of SYBR green, can be collected for further processing,while those slugs that do not fluoresce can be sent to a wastecollection. Similarly, slugs containing amplicons derived from more thanone template can also be sent to waste collection or otherwise preventedfrom being subjected to unnecessary further analysis. Further processingcan comprise, for example, depositing each individual aqueous slug ontosurface 1272, and/or performing cycle sequencing reactions. Diversion ofsample can occur, for example, prior to thermal-cycler 1250, afterthermal-cycler 1250, and/or proximal to tip 1186.

Similar to the embodiments shown in FIGS. 11 and 12, sample can bedispensed into channels in a sample device 1304, as illustrated in FIG.13. The channels can comprise moieties that bind nucleic acids ofinterest. Once samples are bound to the surface of the channel, adesired reaction can be performed while maintaining the samples ofinterest at a given position in the channel, and/or a wash or rinse canbe performed. In some embodiments, a top cover can be disposed on thetop of sample device 1304 so that an enclosed channel can be formedthrough which, for example, a rinse fluid can flow, for example, underpressure A reaction mixture can be introduced into the sample collectiondevice through inlet port 1300 which can be in fluid communication witha channel 1306. The mixture can be washed out through outlet port 1302which is also in fluid communication with channel 1306. Location of thedesired reactive products can be determined by, for example,fluorescence and the samples can be injected into a conduit for the usein step “C” of the process, as shown in FIG. 14.

FIG. 15 is a simplified illustration of a generalized method foranalyzing sequencing products deposited on a substrate. In “A,”amplified nucleic acids can be deposited from a conduit in a controlledfashion, for example, in a rastered pattern, onto a substrate. Thisdeposition of amplified nucleic acids continues at “B.” At “C,” samplescan be detected with a detector 1500 and at “D” the samples can be movedfrom the electrically conductive surface of a substrate into conduitsfor further processing or analysis, for example, by capillaryelectrophoresis. Intermediate steps, for example, a rinse step, can beperformed and/or an injection fluid can be introduced. This can occurwhen a relative potential is provided to the electrically conductivesurface, for example, a negative charge to the surface, and a positivecharge to the end of the capillary electrophoresis tube, as illustratedin “D”.

According to various embodiments, the positions or locations ofsequencing products on other samples of interest on the substrate can beidentified by their fluorescence. If fluorescence is observed, thenbinding of the DNA to the substrate has occurred and a conduit can bepositioned immediately adjacent to the sequencing product as indicatedat “C.” A circuit can be completed between the substrate and theconduits, for example, by liquid or a gel being applied to thesubstrate. An exemplary liquid can comprise an injection fluid asdescribed herein. In various embodiments, the circuit can be completedby small amounts of gel that can be extruded from the conduit of acapillary electrophoresis apparatus, that makes contact with thesubstrate, for example, as a conduit is heated, as shown in FIG. 16. Anelectrical potential can be applied to the substrate and sequencingproducts can be electrokinetically injected into the conduits.

FIG. 16 illustrates an enlarged view illustrating sequencing productsmigrating from the electrically conductive surface into a conduit 1600filled with an electrophoretic separation medium 1602, after a potentialhas been applied to the conductive surface. The conduit can be part of acapillary electrophoretic analyzer. In various embodiments, for example,an ABI 310, ABI 3130, ABI 3130xl, ABI 3700, ABI 3730, or ABI 3730xlcapillary electrophoretic analyzer (available from Applied Biosystems,Foster City, Calif.) can be used for sequencing the products beinginjected in to the conduit.

According to various embodiments, samples from the conduit as shown, forexample, in FIG. 11 or 12, can be deposited on the substrate in adeliberate pattern with respect to the surface on which the samples arebeing deposited. Relative motion between the conduit and the surface canbe achieved by maintaining the surface stationary and moving the conduitor, alternatively, keeping the conduit stationary while moving thesurface, or moving both.

According to various embodiments, a carrier can support the substrateand is mounted for reciprocating motion with respect to the conduit toform one axis of a raster. Of course, the substrate can be fixed withthe conduit arranged to sweep across the substrate in a raster patter. Apropulsion system can generate forces for moving the carrier to aposition. A servo system responsive to an output signal can be providedfor commanding the propulsion system to move the carrier at asubstantially constant speed in a given region or throughout the entiresubstrate. In some embodiments, an open-loop stepper motor system can beused. A control system responsive to the output signal can be providedto modulate a sample deposition period reciprocally to carrier speed toachieve substantially constant movement per sample. The speed ofmovement of the carrier relative to the conduit can be adjusted to takeinto account removal of unwanted discrete-volumes and spacing fluid to awaste receptacle. In various embodiments, if the carrier is movedrelative to a stationary conduit tip 1186, it may not be necessary toalso have various components of the collection device, for example,drive unit 1196.

According to various embodiments, a position sensor, which is monotonicand repeatable, can include, but is not limited to, a counting positionencoder, optical encoder, magnetic encoder, or a capacitive encoder. Thepropulsion system can comprise a motor, voice coil, a galvanometer, agas jet or a graphite piston in a glass cylinder powered by a gas orliquid.

According to various embodiments, PCR products or sequencing reactionproducts can be analyzed by capillary electrophoresis as described inU.S. Pat. No. 5,891,313 to Johnson et at, which is incorporated hereinin its entirety by reference. Sequencing reaction products injected froma sample apparatus can be analyzed in a sieving or non-sieving medium.Sequencing reaction products can also be analyzed by using a capillaryelectrophoresis protocol in an ABI PRISM™ 310 genetic analyzer, or byseparating bands of analytes on a 4.5%, 29:1 acrylamide:bis acrylamide,8 M urea gel prepared for an ABI 377 Automated Fluorescence DNASequencer, or in a higher throughput florescence-based automatedcapillary electrophoresis instruments such as the ABI 3100, ABI 3700,and ABI 3730xl (all available from Applied Biosystems, Foster City,Calif.). Sequence data can be analyzed with GeneScan Software fromApplied Biosystems.

According to various embodiments, genotyping can be carried using thesystems and methods described herein, for example, genotyping asdescribed in Wenz, H. et al. (1998) Genome Res. 8:69-80, which isincorporated herein in its entirety by reference.

FIG. 14 provides a simplified illustration showing attachment of anamplicon to the electrically conductive surface, for example, a gold orgold-coated surface. An amplicon can be deposited or dispensed onto asurface as illustrated at “A” and “B.” Further details of the processare provided in FIG. 14 at “C” to “G.” A double-stranded ampliconcomprising a thiol group can bind to the gold surface through the thiollinkage as illustrated at “C.” The double stranded amplicon is denatured(as illustrated at “D”) and sequence primer is added as illustrated at“E” such that a sequence reaction can be conducted as illustrated at“F.” This can occur at each of the spots illustrated at “G.” Once thereactions are completed, the products can be washed and dried and theninjected as shown in FIGS. 15 and 16. Alternatively, or in addition,washing, rinsing, and/or drying of the surface can be done at othertimes in the process as deemed most appropriate by those of skill in theart. In various embodiments, rather than having a thiol linkage betweenDNA and the substrate, other methods of attachment to the substrate canbe used. For example, either a biotin or strepavidin molecule can beattached to the electrically conductive surface and the correspondinglinker pair can be attached to the terminus of the nucleic acid moleculeto be attached to the substrate.

FIG. 17 illustrates aqueous-sample-discrete-volumes 1706, spaced-apartfrom one another by spacing fluid 1704, flowing down a conduit 1702.Conduit 1702 can comprise an electrically conductive surface and theslugs can comprise samples that can be bound to the surface. The samplescan then be washed and subjected to sequencing reactions after which theslugs can be electrokinetically injected or electrically migrated into,for example, capillary electrophoresis injector 1700 when an electricpotential is applied between the electrically conductive surface and theend of the tube opposite the end shown.

According to various embodiments, the method can comprise subjecting anattached amplicon or sets of attached amplicons to a sequencingreaction. Exemplary sequencing reactions can comprise a stepwisesequencing reaction, a forward/reverse, reverse/forward sequencingreaction, or a Sanger cycle-sequencing reaction. In various embodiments,reverse/forward or forward/reverse sequencing can comprise reactionswith at least one polynucleotide primer.

According to various embodiments and as illustrated in FIG. 18, anelectro-wetting manipulation system 1800 is provided and comprises anelectro-wetting plate 1802 on which a processed droplet 1804 can bemanipulated and moved by electro-wetting action to a pick-up location1828 on electro-wetting plate 1802. Drop 1804 can be made to traverse atransfer pathway 1808 moving from one independently controlledelectro-wetting location or spot 1810 to another through an appropriateapplication of potential to the spots 1810 controlled by anelectro-wetting pathway control unit 1822. While a single pathway 1808is shown, it is to be understood that a variety of pathways are providedon electro-wetting plate 1802 such that a drop can be moved to any of anumber of pick-up locations 1812, 1814, 1816, 1818, and 1820. At pick-uplocation 1828, drop 1804 can be taken up into an injector of a capillaryelectrophoresis apparatus. Deposition on electro-wetting plate 1802 canoccur through a distal discharge tip 1826 of animmiscible-fluid-discrete-volume-forming conduit 1824. In someembodiments, drop 1804 comprises the output of animmiscible-fluid-discrete-volume processing conduit as described herein.In some embodiments, a number of drops 1804 can be brought from a singleor multiple output conduits to a number of points or locations and thepoints or locations can correspond to the spacing of a 96-well or384-well microtiter plate, or, for example, to be lined-up with aninjector array of a capillary electrophoresis apparatus. In someembodiments, the points or locations can comprise a gold surface so thatthiol chemistries as described herein, can be performed. Optionally,reagent supply locations can also be provided on the surface of theplate so that reagents, if needed, can be moved into appropriatepositions by electro-wetting forces.

Further details about generating such a voltage gradient and themanipulation of fluid droplets by electro-wetting can be found, forexample, in U.S. Pat. No. 6,629,826 B2 to Yoon et al., which isincorporated herein in its entirety by reference.

In some embodiments, all drop moving or transfer, on electro-wettingplate 1802, can be done under an oil or spacing fluid overlay.Alternatively, a cover can be implemented at a small fixed distancespaced from the electro-wetted surface such that the use of oil can beeliminated and greater accuracy can be achieved. In some embodiments,each transfer pathway can optionally be washed or rinsed between a fluidmanipulation process. In some embodiments, two or more dropl or portionscan be transferred from two or more locations, and merged together, forexample, at pick-up location 1828, so that a combination of drops cansimultaneously be injected, for example, into a capillaryelectrophoresis capillary injector.

In some embodiments, the methods, apparatuses, and/or systems to providethe extraction or collection of samples contained inimmiscible-fluid-discrete-volumes within a conduit, for example, a tube,capillary, channel, open channel, or other conduit, without the need toeject individual immiscible-fluid-discrete-volumes from the conduit, areprovided. The methods, apparatuses, and/or systems can use migrationproperties of DNA molecules or other charged analytes in the presence ofapplied electric fields. For example, the methods, apparatuses, andsystems can use electrophoretic properties to achieve sample collectionor extraction. In various embodiments of the present teachings, thesample need not be migrated or extracted from aimmiscible-fluid-discrete-volume of material, but can rather be migratedor extracted from samples in other forms in a conduit, for example, froma continuous stream of flowing sample that is not separated intoimmiscible-fluid-discrete-volumes. En some embodiments, an appliedelectric field influences charged analytes to migrate in a directiontransverse to the conduit, for example, through a hole formed in asidewall of a conduit.

According to various embodiments, a flow in a capillary, tube, or otherconduit can be laminar with a velocity profile along the axial directionof the conduit, with little or no velocity component in the radialdirection. Thus, a hole or puncture in the wall of the tube or conduitmight not result in flow or leakage through the hole, if the pressureinside the tube or conduit is not large enough to overcome the surfacetension of a liquid trying to move through the hole. Pressures can bematched so that oil or spacing fluid does not leak through the holes. Insome embodiments, an electrode can pass through or be inserted into ahole in the sidewall of a conduit and be flush with, recessed from, orprotruding from, the inner surface of the conduit wall.

Sample transfer methods, apparatuses, and/or systems disclosed hereincan provide sample collection from a conduit while preservingimmiscible-fluid-discrete-volume integrity, with the exception of samplecomponents collected or removed from theimmiscible-fluid-discrete-volume. This is beneficial in cases where theimmiscible-fluid-discrete-volumes will be used in subsequentapplications that require immiscible-fluid-discrete-volume integrity tobe maintained in the conduit. The immiscible-fluid-discrete-volume canremain intact after removal of a potential that in some cases causes thesurface to be wetted.

According to various embodiments, the methods of the present teachingscan be integrated with a DNA sequencing apparatus, for example, using afluid communication to such an apparatus. When the method involves usingsuch an apparatus, the conduit outlet can be fluidly communicated with aDNA separation channel, and the DNA can be electrokinetically injectedor migrated into the DNA separation channel. Thereafter, DNA separationcan be performed, for example, with or without a separation matrixmaterial in the channel.

According to various embodiments, methods of sample collection orextraction from a immiscible-fluid-discrete-volume can include directedsample collection. For example, if a positive electrode is placed in awell, a negatively charged sample component can be attracted to ortravel toward that electrode. According to various embodiments, a pairof small openings in a wall of aimmiscible-fluid-discrete-volume-carrying conduit can allow anelectrical current to be conducted through an aqueousimmiscible-fluid-discrete-volume in theimmiscible-fluid-discrete-volume-carrying conduit, and negativelycharged molecules can migrate from the immiscible-fluid-discrete-volumetoward a positively charged electrode. In some embodiments, the fieldcan enable the fluid to wet an electrode surface as occurs inelectro-wetting, providing at least an initial electrical contact.

According to various embodiments, multiple wells can be provided, eachwell with an electrode that can be switched on and off independently ofthe electrodes in the other wells. According to such embodiments in oneregard, DNA can be transferred from a conduit to a selected well byswitching on the electrode at that particular well. In some embodimentsthe electrodes can all be switched on and off together to permitsimultaneous injection into a set of analyzer injectors. Spacing fluidcan be added between volumes or slugs so that they can be made toline-up with holes.

FIG. 19 is a schematic illustration of an electrokinetic samplecollection system 1900 according to various embodiments. System 1900 cancomprise a conduit 1902 in the form of a conduit that contains spacingfluid 1908 and aqueous immiscible-fluid-discrete-volumes 1910. Eachaqueous immiscible-fluid-discrete-volume 1910 can comprise DNA moleculesor other charged molecules that are capable of migration in an electricfield. Conduit 1902 can comprise pairs of holes and electrodes atvarious locations there along. In some embodiments a single hole isprovided and an electrode is inserted through the wall of the conduitand can be flush with, set-back from, or protruding from, the inside ofthe conduit and a single analyte collection chamber.

As shown in FIG. 19, the pairs of holes formed in conduit 1902 can be influid communication with a single or with multiple charged analytecollection chambers or compartments, for example, in fluid communicationwith a plurality of wells. The chambers and compartments house or arecomprised of electrodes and are also referred to herein as electrodehousing chambers. Different pairs of electrodes, holes, and/or wells canbe located at different positions along the length of conduit 1902.According to various embodiments, each of the pairs of electrodes can beswitched on and off independently, such that one can transfer DNA orother charged analytes to a selected well by switching on an eiectrodepair comprising at least one electrode at that particular well. Invarious embodiments, a single position along the conduit 1902 can be theonly position comprising a pair of holes and electrodes for chargedanalyte collection.

DNA samples can be collected from the aqueousimmiscible-fluid-discrete-volumes 1910 in conduit 1902 by, for example,electrokinetic migration, electroosmotic migration, and/orelectrophoretic migration, of negatively-charged DNA molecules. As shownat the left side of FIG. 19, according to various embodiments, twoopenings or holes 1916 and 1918 can be created through opposite sides ofthe wall of conduit 1902. Electrodes 1904 and 1906 can be placed inrespective charged analyte collection chambers 1912 and 1914 alignedwith openings 1916 and 1918, respectively. One or more of the aqueousimmiscible-fluid-discrete-volumes 1910 can be brought into conduitsection 1920 and aligned with openings 1916 and 1918. In variousembodiments, flow through conduit 1902 can be stopped to allowelectrophoresis of the desired materials out of the desired aqueousimmiscible-fluid-discrete-volumes 1910. In other various embodiments,flow through conduit 1902 can be maintained at, or reduced to, asufficiently slow velocity or flow rate to permit movement of a desiredanalyte from conduit 1902 into charged analyte collection chambers 1912and/or 1914 when voltage is applied to the respective electrodes.Application of an electric field formed from electrodes 1904 and 1906can cause charged molecules 1926 to migrate from the aqueousimmiscible-fluid-discrete-volume 1910 toward the electrode with oppositepotential 1904 or 1906. In some embodiments, and as shown, electrodes1904 and/or 1906 can be disposed outside of conduit 1902. In variousembodiments, only one of electrodes 1904 and 1906 can be placed outsideconduit 1902, and the opposite electrode can be integrated into theinner sidewall of conduit 1902. In embodiments where electrode 1904 hasa positive potential, negatively charged DNA molecules in one or more ofaqueous immiscible-fluid-discrete-volumes 1910 can move toward electrode1904 and migrate into charged analyte collection chamber 1912. Whenelectrode 1906 is negatively charged, positively charged molecules canmigrate to charged analyte collection chamber 1914. Such an arrangementcan allow for DNA or other charged analyte sample collection whileotherwise preserving the integrity of the aqueousimmiscible-fluid-discrete-volumes 1910.

According to various embodiments, multiple electrokinetic migrations canbe performed from the same immiscible-fluid-discrete-volume. Since theamount of charged analyte that migrates generally correlates with theapplied electric field strength and time, the process can be controlledso that portions of sample in a immiscible-fluid-discrete-volume can becollected into different collection chambers or compartments, ordifferent portions can be collected at different times during samplemigration in the conduit or an adjoining chamber or channel, bycontrolling the application of the applied electric fields. In variousembodiments, a sample from one chamber or compartment can be migratedinto another chamber or compartment.

According to various embodiments, a high degree of serialism orparallelism in sample extraction from multipleimmiscible-fluid-discrete-volumes can be achieved, as, for example,illustrated in FIG. 20. Given information pertaining to the spacingbetween aqueous immiscible-fluid-discrete-volumes in a conduit, thepairs of holes formed in the conduit can be fabricated at appropriatedistances apart such that multiple immiscible-fluid-discrete-volumes canbe subjected to electrokinetic migration simultaneously, offering a highlevel of multiplexed sample collection. FIG. 20 illustrates a system forsuch a multiplexing scheme using electrokinetic sample collection fromaqueous immiscible-fluid-discrete-volumes 2010 in a conduit 2002.Spacing fluid 2008 is also illustrated and can be used to space-apartthe aqueous immiscible-fluid-discrete-volumes. Migration of DNAmolecules 2026 can be targeted to at least one of chambers 2012 a, 2012b, 2012 c, 2012 d, 2012 e, and 2012 f by providing current to at leastone of corresponding electrodes 2004 a, 2004 b, 2004 c, 2004 d, 2004 e,and 2004 f, respectively. A common electrode 2006 can be provided tocomplete a circuit from any one or more of corresponding electrodes 2004a, 2004 b, 2004 c, 2004 d, 2004 e, and 2004 f. DNA 2026 from samplechamber 2012 can migrate through opening 2016 in conduit 2002 intochamber 2012 and then be further migrated into at least one of chambers2012 a, 2012 b, 2012 c, 2012 d, 2012 e, or 2012 f. In some embodiments,different potentials can be applied to the different electrodes 2004a-2004 f, and/or the electrophoretic separation channels leading tochambers 2012 a-2012 f can be different from one another, for example,so that different analytes can be collected in the different chambers.In some embodiments, the separation channels leading to chambers 2012a-2012 f can have different lengths from one another, can containdifferent separation media from one another, and/or can otherwise bedifferent from one another. In some embodiments, the electrodes 2004a-2004 f can be powered individually, in combination with electrode2006, for example, such that analytes from six different aqueousimmiscible-fluid-discrete-volumes can be collected respectively in thesix different chambers or wells 2012 a-2012 f. In various embodiments,DNA 2026 can migrate toward electrode 2006 and into chamber 2014 fromconduit 2002, if the current is reversed.

The electrokinetic sample collection fromimmiscible-fluid-discrete-volume 2010 in conduit 2002 can result inmigration of DNA molecules into corresponding chambers serially,simultaneously, or in any Other desired spatial or temporal order.

In the embodiments shown at least in FIGS. 19 and 20, a plurality ofholes or openings can be used for simultaneous injection into aplurality of injectors, for example, 16 holes, openings, or locations,for electrokinetic migration can be spaced apart in a two by eight arrayspaced at a pitch equal to the pitch of a 16-capillary injector of a16-capillary capillary electrophoresis apparatus. As such, the injectorcan interface with the migration holes, openings, or locations.

According to various embodiments and as illustrated in FIG. 21, conduit2102 can contain spacing fluid 2110 and aqueousimmiscible-fluid-discrete-volumes 2108. According to variousembodiments, charged molecules 2126 can be transferred, for example, bycausing negatively charged DNA molecules to migrate through openings2112 and 2114 from lower conduit 2102 into upper conduit 2104. If twoconduits are lined-up next to one another, it is possible to transfercharged molecules from one conduit to the other by exploitation ofsample stacking characteristics, for example, as shown in FIG. 21. Byproviding the solution in one of the conduits with a high ionconcentration, for example, as shown in top conduit 2104, chargedmolecules in the lower conduit can accumulate or stack-up at theinterface of the two conduits and be migrated into the top conduit.

According to various embodiments and as illustrated in FIGS. 22A and22B, a system and method similar to that shown in FIGS. 17 and 16,respectively, is provided. A sample in a conduit can comprise componentsuseful for Sanger sequencing with dye terminators, for instance, usingneutrally charged dye-ddNTPs. Using methods and apparatus describedherein, including a system 2200 as shown, minimal or no sequencingclean-up is necessary during the sequencing protocol. In variousembodiments as illustrated in FIG. 22A, upon application of a currentselectively delivered to one or more capillaries via switches 2230,2232, and the like, which in-turn are connected to an electrical powersource, charged molecules 2226 can be made to migrate from the conduit2202 into a injector 2212 at a junction 2216. Junction 2216 is definedby the intersection of wall 2213 of injector 2212 and top wall 2208 ofconduit 2202. The bottom wall 2206 of conduit 2202 can serve as anegative electrode as shown in FIG. 22A. The charged molecules 2226 cancomprise DNA fragments comprising one or more dyes in an aqueousimmiscible-fluid-discrete-volume 2210. Aqueousimmiscible-fluid-discrete-volumes 2210 can be spaced apart from oneanother by spacing fluid 2208, as shown. Any remaining neutrally chargeddye molecules can remain in the conduit 2202 and not migrate into theinjectors 2212. In other embodiments, a charged dye molecule can be usedand both the dye and DNA fragments comprising the dye can migrate intoone or more injectors 2212 or other chambers or compartments for furtherseparation, purification, detection, or other processing, as desired.

According to various embodiments, controllable valves can be used forpermitting, interrupting, or otherwise controlling, fluid flow throughone or more of the capillaries, tubes, orifices, through holes, and thelike conduits described herein. Exemplary controllable valves caninclude, but are not limited to, valves comprising a stator (or body)and rotor (or plug) structure, for example, any of the structures shownin FIGS. 23-28. Out-putting schemes to collect desired discrete-volumesand remove undesired discrete-volumes can use one or more rotary valvesas shown in FIGS. 23-28, according to various embodiments.

As shown in FIG. 23, valve 2300 can comprise a stator 2302, and a rotor2304. Rotor 2304 can rotate, for example, about a central axis ofrotation 2306, to orient the rotor such that valve 2300 is in an openstate (as shown in FIG. 23), in a closed state (as shown in FIG. 25), orin an intermediate state. In the open state shown in FIG. 23, a centralbore or through hole 2308 through rotor 2304 is aligned with bores orthrough holes 2310 and 2311 formed in stator 2302. Through hole 2310 instator 2302 can be aligned with a larger recess 2312 in stator 2302, inwhich recess 2312 and first conduit 2314, for example, a tube, cansnugly fit and/or be adhered or otherwise connected. Likewise, throughhole 2311 can be aligned with and in fluid communication with a largerrecess 2316 also in stator 2302. Recess 2316 can accommodate a secondconduit 2318 fit, adhered, or otherwise connected to stator 2302. Insome embodiments, each of through holes 2308, 2310, and 2311, and eachof recesses 2312 and 2316, has a circular cross-section although othercross-sections can be used.

As shown in FIG. 25, rotation of rotor 2304 can interrupt fluidcommunication between conduits 2314 and 2318 and rotation of rotor 2304can form a fluid communication through two different conduits 2514 and2518. A programmable drive unit can be provided to actuate rotation ofrotor 2308. By filling through hole 2308 with a first fluid, forexample, flowing through conduits 2314 and 2318, and then rotating rotor2304, with a portion of the first fluid captured in through-hole 2308,to form a communication with conduits 2514 and 2518, the portion offirst fluid captured in through-hole 2308 can be disposed into a flow ofa second fluid through conduits 2514 and 2518, for example, wherein thesecond fluid is immiscible with the first fluid. Repeated operations ofsuch action can result in the formation of a plurality ofimmiscible-fluid-discrete-volumes spaced apart from another by animmiscible spacing fluid, similar to the methods of formation describedin connection with the slider system shown in FIGS. 21A-21F herein.Similarly, a slug can be chopped or divided into two or more portions,using such a method, and the two or more portions can then be output forseparate further processing.

In valve 2400 shown in FIG. 24, the combination of a smaller diameterthrough hole and a larger diameter recess in each side (left and rightas shown) of a stator 2402 has been replaced with single through holes2406 and 2407 on opposing sides of a rotor 2404. In the embodimentsshown in FIG. 24, conduits 2408 and 2409 are accommodated, respectively,and fit snugly within, through holes 2406 and 2407, for example,adhered, such that the ends of conduits 2408 and 2409 closest to rotor2404 abut rotor 2404. Valve 2400 is shown in an open position withthrough hole 2410 of rotor 2404 being aligned with and sharing the samecross-sectional dimensions and shape as the interiors of conduits 2408and 2409.

In the valve embodiment shown in FIG. 26, a valve 2600 comprises threethrough passages in stator 2602, which accommodate conduits 2614, 2618,and 2620. Rotor 2604 is provided with two intersecting through holes2622 and 2624. Depending upon the orientation of rotor 2604, forexample, determined by rotation about a central axis of rotation, valve2600 can assume a closed position, a straight-line open position, or theY-intersection position shown. When utilized in a Y-intersectionposition such as shown in FIG. 26, one or more fluids entering theintersection in the middle of rotor 2604 from conduit 2614 can mergewith one or more miscible and/or immiscible fluids entering theintersection from conduit 2620, such that a resulting combined flow offluid can be made to move inside conduit 2618 in a direction away fromthe intersection.

In some embodiments, a first fluid to be divided intoimmiscible-fluid-discrete-volumes, for example, an aqueous slug fluid,can enter the intersection from either of conduits 2614 or 2620, and animmiscible spacing fluid can enter the intersection through the other ofconduits 2614 and 2620, to generate immiscible-fluid-discrete-volumes ofthe first fluid spaced by the spacing fluid. In some embodiments,reagents or additional components can be merged into existing fluids oraqueous immiscible-fluid-discrete-volumes entering the intersection, forexample, such that the size and/or number of reagents in animmiscible-fluid-discrete-volume can be increased at the intersection.By turning rotor 2604 about 45° counterclockwise, a fluid communicationcan be provided between only conduit 2614 and 2618, and fluidcommunication with conduit 2620 can be interrupted.

Another controllable valve that can be implemented in many of thesystems and methods described herein, is the valve shown in FIGS. 27 and28. Valve 2700 comprises a stator 2702 and a rotor 2704 that comprisestwo through holes 2706 and 2722. In a first orientation of rotor 2704,as shown in FIG. 27, through hole 2706 is aligned with through holes2708 and 2718 of stator 2702 and provides a fluid communication betweenconduit 2712 and conduit 2714. In FIG. 27, through hole 2722 in rotor2704 is in a closed, non-operative, position.

As shown in FIG. 28, by rotating rotor 2704, through hole 2722 can bealigned with through hole 2718 and through hole 2724 in stator 2702 suchthat conduit 2714 is in fluid communication with conduit 2720 and fluidcommunication to conduit 2712 is interrupted.

As can be seen from FIGS. 23-28, a method is provided that comprisesmerging together at an intersection of a first conduit and a secondconduit a first fluid and a second fluid, the first fluid comprising aspacing fluid and the second fluid comprising animmiscible-discrete-volume-forming fluid that is immiscible with thefirst fluid, such that a set of immiscible-fluid-discrete-volumes of thesecond fluid are formed in a third conduit in fluid communication withthe first conduit and the second conduit, wherein eachimmiscible-fluid-discrete-volume of the set is spaced apart from otherimmiscible-fluid-discrete-volumes by the first fluid, and at least oneof the first fluid, the second fluid, and the set ofimmiscible-fluid-discrete-volumes flows through a rotary valvecomprising a stator and a rotor. In some embodiments, at least a portionof each of the first conduit, the second conduit, and the third conduitis disposed in the rotor, and the intersection comprises an intersectionof the three portions in the rotor. In some embodiments, the rotor cancomprise at least two independent, non-intersecting through holes formedtherein, wherein one of the at least two through holes is in fluidcommunication with the first conduit, and another of the at least twothrough holes is in fluid communication with the second conduit.

As shown in FIG. 29 according to various embodiments a valve can beprovided that has a slider 2908 in a housing 2910 that moves to eitherform a three-way intersection between three conduits 2902, 2904, and2906, or to interrupt fluid communication between conduits 2902 and2904, and thus, to interrupt fluid communication between either conduit2902 or conduit 2904, and conduit 2906.

Through the use of various combinations of the valves shown in FIGS.23-29, any of a variety of fluid processing pathways can be effectuatedin a multi-pathway system such as the multi-pathway systems describedherein. Selected pathways for collection versus waste removal can beprovided by appropriate control of rotary or other valves in suchpathways.

According to various embodiments, the present teaching can comprise theplacement of processed immiscible-fluid-discrete-volumes in a sampletray, for example, a multi-well plate. Theimmiscible-fluid-discrete-volumes placed on the sample tray can besubjected to further analysis, for example, capillary electrophoresis.It can be desirable to select only certainimmiscible-fluid-discrete-volumes, from a set ofimmiscible-fluid-discrete-volumes, for analysis. The present teachingscan comprise a selection process whereby onlyimmiscible-fluid-discrete-volumes containing analytes of interest areselected for placement on the sample plate. For example, onlyimmiscible-fluid-discrete-volumes that have successfully undergone anucleic acid amplification reaction can be selected for placement on thesample tray. A nucleic acid amplification reaction can fail for a numberof reasons, for example, the lack of a suitable template, impropertemperature control, or improper/missing reactants.

According to some embodiments, and as illustrated in FIG. 30, thepresent teachings can comprise a system 3000 for separating selectedimmiscible-fluid-discrete-volumes from a set ofimmiscible-fluid-discrete-volumes. System 3000 can comprise a dispensingconduit 3002, for dispensing immiscible-fluid-discrete-volumes 3001.Dispensing conduit 3002 can have a consistent diameter. In someembodiments, dispensing conduit 3002 can have a diameter that isgradually reduced towards a discharge tip 3004, and conduit 3002 canfurther comprise a lip around discharge tip 3004 (not shown). System3000 can comprise a positioning unit 3006 for positioning dispensingconduit 3002. For example, dispensing conduit can be moved in X, Y,and/or Z directions.

According to various embodiments, system 3000 can comprise a detector3008. Detector 3008 can comprise an infra-red slotted optical switch, aphotodiode, a fluorescence detector, a PMT, a photodiode, or any othersuitable detector. Detector 3008 can comprise a lens 3010, a beamsplitter 3012, a light source 3014, and/or a photo-detector 3016.Detector 3008 can be a refractive detector capable of detecting thepresence, size, and/or speed of an immiscible-fluid-discrete-volumepresent in dispensing conduit 3002. Detector 3008 can detect thedifferences between volumes of, for example, air, water, and/or oil. Insome embodiments, system 3000 can comprise multiple detectors (notshown). The multiple detectors can be a known distance apart alongdispensing conduit 3002. The detectors can be used to determine thespeed of an immiscible-fluid-discrete-volume by measuring the time ittakes for the immiscible-fluid-discrete-volume to pass from one detectorto the next. A signal from one or more detectors can be sent topositioning unit 3026 to appropriately position discharge tip 3004 foreither discrete-volume collection or waste removal.

According to some embodiments, system 3000 can comprise a waste removalblock 3018. Waste removal block 3018 can comprise a through-hole 3020.Waste removal block 3018 can comprise a waste removal conduit 3022.Waste removal conduit 3022 can be in fluid communication withthrough-hole 3020. Waste removal conduit 3022 can further comprise anaperture 3021. Aperture 3021 can be in fluid communication withthrough-hole 3020. Aperture 3021 can be used to visually inspectdischarge tip 3004 through through-hole 3020. System 3000 can comprise avacuum source 3030. Vacuum source 3030 can be in fluid communicationwith waste removal conduit 3022. System 3000 can comprise a sample tray3024. Sample tray can comprise a positioning unit 3026. Positioning unit3026 can move sample tray 3024, for example, in X, Y, and/or Zdirections, or can move waste removal block 3018, or both. Sample tray3024 can be disposed below waste removal block 3018. In someembodiments, the sample tray can be in the form of a tray as illustratedin FIG. 2, 12, or 18, herein.

System 3000 can comprise a control unit 3028. Control unit 3028 can beconnected, for example, electrically connected, to positioning unit3006, detector 3008, positioning unit 3026, and/or vacuum source 3030.Control unit 3028 can comprise a microprocessor or the like. Controlunit 3028 can function to control the elements connected thereto.

According to various embodiments, system 3000 can be used in conjunctionwith a method of selecting and depositing specificimmiscible-fluid-discrete-volumes. For the following selection method,all elements can be controlled by control unit 3028. In some embodimentsthe method comprises lowering dispending conduit 3002 into through-hole3020, of waste removal block 3018. A vacuum can be applied to wasteremoval conduit 3022. Immiscible-fluid-discrete-volumes can be movedtoward discharge tip 3004. Non-selectedimmiscible-fluid-discrete-volumes, and any associated oil spacing fluid,can be sucked out of discharge tip 3004, into waste removal conduit3022, and discarded. The vacuum applied (with appropriate delays asrequired) until an immiscible-fluid-discrete-volume of interest isdetected by detector 3008.

According to some embodiments, the selection method comprises detectingan immiscible-fluid-discrete-volume of interest, then waiting an amountof time before removing the vacuum from waste removal conduit 3022. Theamount of time can be sufficient for theimmiscible-fluid-discrete-volume of interest to move into discharge tip3004. As depicted in FIG. 31, dispensing conduit 3002 can be moved suchthat discharge tip is disposed in or directly above sample tray 3024. Animmiscible-fluid-discrete-volume of interest can then be expelled fromdispensing conduit 3002, into a well of sample tray 3024.

According to various embodiments, sample tray 3024 can be positionedsuch that an empty well is directly below dispensing tip 3004. Sampletray 3024 can be moved, for example, shortly before animmiscible-fluid-discrete-volume is expelled, shortly thereafter, or atany time in between such that an empty well is disposed in the properposition before an immiscible-fluid-discrete-volumes is expelledtherein.

After an immiscible-fluid-discrete-volume has been expelled, thedispensing conduit 3002 can be moved back into its original positionshown in FIG. 30, and the process can begin again.

In some embodiments, a liquid flow can be induced in waste removalconduit 3022 rather than an air vacuum. The liquid flow can function torinse and/or wash discharge tip 3004, and thereby prevent crosscontamination.

1-22. (canceled)
 23. A system comprising: an aqueous sample injectionunit in fluid communication with at least one conduit comprising amaximum inner cross-sectional dimension; a spacing fluid injection unitin fluid communication with the at least one conduit, the aqueous sampleinjection unit and the spacing fluid injection unit in fluidcommunication with the at least one conduit; a control unit adapted toflow an aqueous sample and a spacing fluid from the aqueous sampleinjection unit and the spacing fluid injection unit, respectively, andadapted to inject volumes of aqueous sample and spacing fluid thatrespectively form slugs in the at least one conduit wherein each slughas an outer dimension that is equal to the maximum innercross-sectional dimension of the at least one conduit; an electricallyconductive substrate; and a capillary electrophoretic sequencer adaptedto inject a sample component when a sample component is disposed on theelectrically-conductive surface.
 24. The system of claim 23, wherein theelectrically conductive surfaces comprise at least one channel.
 25. Thesystem of claim 23, wherein the electrically conductive substratecomprises linker moieties adapted to bind to a nucleic acid.
 26. Thesystem of claim wherein the linker moieties comprise a plurality of thesame linker moiety.
 27. The system of claim 23, wherein the electricallyconductive substrate comprises at least one channel.
 28. The system ofclaim 23, wherein the aqueous fluid injection unit and the spacing fluidinjection unit comprise separate units. 29-73. (canceled)
 74. A systemcomprising: an immersion plate, and a layer of a first fluid retained bythe immersion plate; and a conduit comprising a tip and an interior, theinterior comprising a plurality of immiscible-fluid-discrete-volumes ofa second fluid, spaced apart by a spacing fluid that is immiscible witheach of the immiscible-fluid-discrete-volumes, disposed in the interior,wherein the tip is positioned such that when theimmiscible-fluid-discrete-volumes exit the tip, theimmiscible-fluid-discrete-volumes contact the first fluid retained bythe immersion plate, and the second fluid has a different density thanthe first fluid.
 75. A method comprising: dischargingimmiscible-fluid-discrete-volumes from inside a conduit having adischarge tip, through the discharge tip, and into a first fluidretained by an immersion plate, wherein the first fluid is immisciblewith the immiscible-fluid-discrete-volumes and the density of the firstfluid is different than the densities of each of theimmiscible-fluid-discrete-volumes.
 76. The method of claim 75, whereinthe densities of the immiscible fluids of theimmiscible-fluid-discrete-volumes are each greater than the density ofthe first fluid.
 77. The method of claim 75, wherein the first fluidretained by the immersion plate has a surface, and the discharge tip isdisposed below the surface.
 78. The method of claim 75, wherein theimmiscible-fluid-discrete-volumes are spaced apart from one another inthe conduit by a spacing fluid that is immiscible with theimmiscible-fluid-discrete-volumes.
 79. The method of claim 78, whereinthe spacing fluid is the same fluid as the first fluid.
 80. The methodof claim 75, wherein the first fluid comprises an oil.
 81. The method ofclaim 80, wherein the immersion plate comprises hydrophilic featurescovered by the first fluid, at least one of the hydrophilic featurescomprises a gold surface, and one or more of theimmiscible-fluid-discrete-volumes discharged from the conduit is incontact with one or more of the hydrophilic features and comprises asulfhydryl-labeled primer.
 82. The method of claim 81, wherein theimmersion plate further comprises a hydrophobic coating that surroundsone or more of the hydrophilic features. 83-96. (canceled)